From garyfallidis at gmail.com  Thu Jan  3 17:31:37 2019
From: garyfallidis at gmail.com (Eleftherios Garyfallidis)
Date: Thu, 3 Jan 2019 17:31:37 -0500
Subject: [Neuroimaging] [DIPY WORKSHOP 2019 - titanium edition] Registration
 is now open!
Message-ID: <CAN6JmWPVPN6+pNLO3xr0EURfytrZWFB8jPTeV+XyQ-f9wsY_fA@mail.gmail.com>

Hello fellow Neuroimagers!

The *DIPY* <http://dipy.org/> project is hosting an exquisite educational
workshop *March 11-15* at Indiana University, USA. See topics and detailed
information here:
*https://workshop.dipy.org* <https://workshop.dipy.org/>
The workshop will include tutorials from a great range of topics including
tracking, microstructure, and statistical analysis (see all tutorials here
<https://workshop.dipy.org/>). The workshop will also include a data
accelerator where you will be able to analyse your own data together with
the *DIPY* <http://dipy.org/> developers. More than 15 DIPY developers will
be available this year on site to help. All tutorials will run on 3 levels:
novice, intermediate and advanced.

Have in mind that this is a registration-only 5 day event.

The event is co-sponsored by the National Institute of Health (NIH) and the
School of Informatics, Computing and Engineering of Indiana University.

Exciting? Register here <https://workshop.dipy.org/>.

Questions? More than happy to answer any questions you may have here or at
dipy at python.org.

Best regards,
Eleftherios

p.s. Please forward to all interesting parties.
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From arokem at gmail.com  Fri Jan  4 09:23:07 2019
From: arokem at gmail.com (Ariel Rokem)
Date: Fri, 4 Jan 2019 06:23:07 -0800
Subject: [Neuroimaging] failure using DIPY Free Water Elimination DTI
In-Reply-To: <CAL1NnmMxoHER2vdvhTsk4TR2zMtanHfURx=+J-PxqwjTB9p1dw@mail.gmail.com>
References: <CAL1NnmNTd0z+k7-bu1+PSAk_zdcEdK2Yk+jPKAWzC0wt2CUCZA@mail.gmail.com>
 <CA+X4w0zE_wDfF3xFMBcT2ryhherw+esHOS4guhk98q614yT4AA@mail.gmail.com>
 <CAL1NnmMxoHER2vdvhTsk4TR2zMtanHfURx=+J-PxqwjTB9p1dw@mail.gmail.com>
Message-ID: <CA+X4w0wDjWx3idaNyLjjpCwrnj8K7OD1oOS4ZGQTUHK71mxxNg@mail.gmail.com>

Hi Ping,

I can't quite reproduce your error, though I am getting similar errors.
Could you also share the code that you are running?

For the time being, the one thing that I noticed is that there are NaNs in
your data. That might be causing this issue.

Cheers,

Ariel



On Mon, Dec 31, 2018 at 5:43 AM Ping-Hong Yeh <pinghongyeh at gmail.com> wrote:

> Hi Ariel,
>
>  Have you got the chance to look at the DWI data that was attached to the
> previous email?
>
> Thank you for your time.
>
> Ping
>
> On Sat, Dec 29, 2018 at 1:12 AM Ariel Rokem <arokem at gmail.com> wrote:
>
>> Hi Ping,
>>
>> Thanks for your email. Hard to say exactly what is going on without
>> further information. Could you tell us more about the data you are using?
>> How many b-values? How many directions? Any chance you could share the data
>> from the voxel that caused that error to be raised?
>>
>> Thanks!
>>
>> Ariel
>>
>> On Thu, Dec 27, 2018 at 6:55 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>> wrote:
>>
>>> Hi Dipy Users,
>>>
>>>  I've ran into errors "Eigenvalues did not  converge" when using the
>>> free water elimination model,
>>> and here is the error message:
>>>
>>>   File
>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>> line 1615, in _decompose_tensor_nan
>>>     min_diffusivity=min_diffusivity)
>>>   File
>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>> line 1946, in decompose_tensor
>>>     eigenvals, eigenvecs = eigh(tensor)
>>>   File
>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/utils/arrfuncs.py",
>>> line 128, in eigh
>>>     return np.linalg.eigh(a, UPLO)
>>>   File
>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>> line 1291, in eigh
>>>     w, vt = gufunc(a, signature=signature, extobj=extobj)
>>>   File
>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>> line 95, in _raise_linalgerror_eigenvalues_nonconvergence
>>>     raise LinAlgError("Eigenvalues did not converge")
>>> numpy.linalg.linalg.LinAlgError: Eigenvalues did not converge
>>>
>>>
>>> Any suggestions?
>>>
>>> Thank you.
>>>
>>> Ping
>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From pinghongyeh at gmail.com  Fri Jan  4 10:42:10 2019
From: pinghongyeh at gmail.com (Ping-Hong Yeh)
Date: Fri, 4 Jan 2019 10:42:10 -0500
Subject: [Neuroimaging] failure using DIPY Free Water Elimination DTI
In-Reply-To: <CA+X4w0wDjWx3idaNyLjjpCwrnj8K7OD1oOS4ZGQTUHK71mxxNg@mail.gmail.com>
References: <CAL1NnmNTd0z+k7-bu1+PSAk_zdcEdK2Yk+jPKAWzC0wt2CUCZA@mail.gmail.com>
 <CA+X4w0zE_wDfF3xFMBcT2ryhherw+esHOS4guhk98q614yT4AA@mail.gmail.com>
 <CAL1NnmMxoHER2vdvhTsk4TR2zMtanHfURx=+J-PxqwjTB9p1dw@mail.gmail.com>
 <CA+X4w0wDjWx3idaNyLjjpCwrnj8K7OD1oOS4ZGQTUHK71mxxNg@mail.gmail.com>
Message-ID: <CAL1NnmMjJEMFgy20TqRc35egF3-w4GPDjLnW-DW_as61jTG5Bw@mail.gmail.com>

Hi Ariel,

Thank you for your time.
 I've run fslmaths using the syntax of -nan  beforehand, i thought that has
taken care of it.

Here is the script i used,

import dipy.reconst.fwdti as fwdti
Delta = 22.536
delta = 21.908
_Delta = 0.022536
_delta = 0.021908

dname=os.path.join('/data/NEURO2/ping/MUX', id,
'SOA_N270_plus19b0_fwd','data_DIFFPREP_t2acpc_proc_DRBUDDI_proc')
fdwi = join(dname,
'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0_nan.nii.gz')
fbvec = join(dname,
'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0_invY.bvecs') #the final
oriention after TORTOISE is RAS for earlier SOA289 data
fbval = join(dname,
'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0.bvals')

from dipy.io import read_bvals_bvecs
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
from dipy.core.gradients import gradient_table
gtab = gradient_table(bvals, bvecs, big_delta=Delta, small_delta=delta)
img = nib.load(fdwi)
data = img.get_data()
affine = img.affine

#free water
fwdtimodel = fwdti.FreeWaterTensorModel(gtab, fit_method='NLS' )
fwdtifit = fwdtimodel.fit(data, mask=mask)
img = nib.Nifti1Image(fwdtifit.fa, affine)
nib.save(img, join(dname, 'FWdti_FA.nii.gz'))
img = nib.Nifti1Image(fwdtifit.md, affine)
nib.save(img, join(dname, 'FWdti_MD.nii.gz'))
img = nib.Nifti1Image(fwdtifit.ad, affine)
nib.save(img, join(dname, 'FWdti_AD.nii.gz'))
img = nib.Nifti1Image(fwdtifit.rd, affine)
nib.save(img, join(dname, 'FWdti_RD.nii.gz'))
img = nib.Nifti1Image(fwdtifit.f, affine)
nib.save(img, join(dname, 'FWdti_fw.nii.gz'))


On Fri, Jan 4, 2019 at 9:23 AM Ariel Rokem <arokem at gmail.com> wrote:

> Hi Ping,
>
> I can't quite reproduce your error, though I am getting similar errors.
> Could you also share the code that you are running?
>
> For the time being, the one thing that I noticed is that there are NaNs in
> your data. That might be causing this issue.
>
> Cheers,
>
> Ariel
>
>
>
> On Mon, Dec 31, 2018 at 5:43 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
> wrote:
>
>> Hi Ariel,
>>
>>  Have you got the chance to look at the DWI data that was attached to the
>> previous email?
>>
>> Thank you for your time.
>>
>> Ping
>>
>> On Sat, Dec 29, 2018 at 1:12 AM Ariel Rokem <arokem at gmail.com> wrote:
>>
>>> Hi Ping,
>>>
>>> Thanks for your email. Hard to say exactly what is going on without
>>> further information. Could you tell us more about the data you are using?
>>> How many b-values? How many directions? Any chance you could share the data
>>> from the voxel that caused that error to be raised?
>>>
>>> Thanks!
>>>
>>> Ariel
>>>
>>> On Thu, Dec 27, 2018 at 6:55 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>>> wrote:
>>>
>>>> Hi Dipy Users,
>>>>
>>>>  I've ran into errors "Eigenvalues did not  converge" when using the
>>>> free water elimination model,
>>>> and here is the error message:
>>>>
>>>>   File
>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>>> line 1615, in _decompose_tensor_nan
>>>>     min_diffusivity=min_diffusivity)
>>>>   File
>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>>> line 1946, in decompose_tensor
>>>>     eigenvals, eigenvecs = eigh(tensor)
>>>>   File
>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/utils/arrfuncs.py",
>>>> line 128, in eigh
>>>>     return np.linalg.eigh(a, UPLO)
>>>>   File
>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>>> line 1291, in eigh
>>>>     w, vt = gufunc(a, signature=signature, extobj=extobj)
>>>>   File
>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>>> line 95, in _raise_linalgerror_eigenvalues_nonconvergence
>>>>     raise LinAlgError("Eigenvalues did not converge")
>>>> numpy.linalg.linalg.LinAlgError: Eigenvalues did not converge
>>>>
>>>>
>>>> Any suggestions?
>>>>
>>>> Thank you.
>>>>
>>>> Ping
>>>>
>>>> _______________________________________________
>>>> Neuroimaging mailing list
>>>> Neuroimaging at python.org
>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From arnavlohe15 at gmail.com  Fri Jan  4 11:56:03 2019
From: arnavlohe15 at gmail.com (Arnav Lohe)
Date: Fri, 4 Jan 2019 11:56:03 -0500
Subject: [Neuroimaging] Looping through 3D NIFTI Image: Help
Message-ID: <CA+NX+7pzOKp5oVQWKZ5LWVX66Eqdia-wKLVuX8ecU1uOoDmDng@mail.gmail.com>

Dear Neuroimaging List Members,

My name is Arnav Lohe, and I am a junior at Rutgers University working on a
neuroimaging project. I want to write an original piece of code to
calculate the total tissue volume in a (.nii) MRI image, and to do this I
need to loop through the multidimensional array. The loop is what I do not
know how to do. I tried triple indexing, I tried converting the .nii image
into a numpy array, and got nowhere with my approaches. Does someone know
how to loop through the individual voxels and extract the numerical
information inside each one?

https://stackoverflow.com/questions/54031899/how-can-i-loop-through-3d-nifti-image-in-python

I have also posted this to StackOverflow, all additional relevant details
should be there.

Sincerely,
Thanking you,
Arnav Lohe
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From jxrel at hotmail.com  Fri Jan  4 12:29:44 2019
From: jxrel at hotmail.com (=?utf-8?B?Sm9zZSBSZXkgTMOzcGV6?=)
Date: Fri, 4 Jan 2019 17:29:44 +0000
Subject: [Neuroimaging] Looping through 3D NIFTI Image: Help
In-Reply-To: <CA+NX+7pzOKp5oVQWKZ5LWVX66Eqdia-wKLVuX8ecU1uOoDmDng@mail.gmail.com>
References: <CA+NX+7pzOKp5oVQWKZ5LWVX66Eqdia-wKLVuX8ecU1uOoDmDng@mail.gmail.com>
Message-ID: <AM4PR05MB3490098A17D3E78781DE9A04A68E0@AM4PR05MB3490.eurprd05.prod.outlook.com>

Using nilearn you could do:

niimage = nilearn.image.load_img(?path?)
Voxels = niimage.get_data()

You get a numpy array, with Voxel[i,j,k] would allow you to access any voxel

Voxels[:,x,y] to acces a single line

Voxels[:,:,x]  to access any slice

Or to iterate over all voxels

for i ....
     for j ....
          for k .....
                Voxels[i,j,k]


On 4 Jan 2019, at 17:58, Arnav Lohe <arnavlohe15 at gmail.com<mailto:arnavlohe15 at gmail.com>> wrote:

Dear Neuroimaging List Members,

My name is Arnav Lohe, and I am a junior at Rutgers University working on a neuroimaging project. I want to write an original piece of code to calculate the total tissue volume in a (.nii) MRI image, and to do this I need to loop through the multidimensional array. The loop is what I do not know how to do. I tried triple indexing, I tried converting the .nii image into a numpy array, and got nowhere with my approaches. Does someone know how to loop through the individual voxels and extract the numerical information inside each one?

https://stackoverflow.com/questions/54031899/how-can-i-loop-through-3d-nifti-image-in-python

I have also posted this to StackOverflow, all additional relevant details should be there.

Sincerely,
Thanking you,
Arnav Lohe
_______________________________________________
Neuroimaging mailing list
Neuroimaging at python.org<mailto:Neuroimaging at python.org>
https://mail.python.org/mailman/listinfo/neuroimaging
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From arokem at gmail.com  Fri Jan  4 13:12:52 2019
From: arokem at gmail.com (Ariel Rokem)
Date: Fri, 4 Jan 2019 10:12:52 -0800
Subject: [Neuroimaging] failure using DIPY Free Water Elimination DTI
In-Reply-To: <CAL1NnmMjJEMFgy20TqRc35egF3-w4GPDjLnW-DW_as61jTG5Bw@mail.gmail.com>
References: <CAL1NnmNTd0z+k7-bu1+PSAk_zdcEdK2Yk+jPKAWzC0wt2CUCZA@mail.gmail.com>
 <CA+X4w0zE_wDfF3xFMBcT2ryhherw+esHOS4guhk98q614yT4AA@mail.gmail.com>
 <CAL1NnmMxoHER2vdvhTsk4TR2zMtanHfURx=+J-PxqwjTB9p1dw@mail.gmail.com>
 <CA+X4w0wDjWx3idaNyLjjpCwrnj8K7OD1oOS4ZGQTUHK71mxxNg@mail.gmail.com>
 <CAL1NnmMjJEMFgy20TqRc35egF3-w4GPDjLnW-DW_as61jTG5Bw@mail.gmail.com>
Message-ID: <CA+X4w0y921S3hRPQ7PMzTOBz-=Tw33xTojpQmqL0JkN6DnAj9g@mail.gmail.com>

On Fri, Jan 4, 2019 at 7:42 AM Ping-Hong Yeh <pinghongyeh at gmail.com> wrote:

> Hi Ariel,
>
> Thank you for your time.
>  I've run fslmaths using the syntax of -nan  beforehand, i thought that
> has taken care of it.
>

I believe it's still there. My script crashed on that.


> Here is the script i used,
>
> import dipy.reconst.fwdti as fwdti
> Delta = 22.536
> delta = 21.908
> _Delta = 0.022536
> _delta = 0.021908
>
> dname=os.path.join('/data/NEURO2/ping/MUX', id,
> 'SOA_N270_plus19b0_fwd','data_DIFFPREP_t2acpc_proc_DRBUDDI_proc')
> fdwi = join(dname,
> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0_nan.nii.gz')
> fbvec = join(dname,
> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0_invY.bvecs') #the final
> oriention after TORTOISE is RAS for earlier SOA289 data
> fbval = join(dname,
> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0.bvals')
>
> from dipy.io import read_bvals_bvecs
> bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
> from dipy.core.gradients import gradient_table
> gtab = gradient_table(bvals, bvecs, big_delta=Delta, small_delta=delta)
> img = nib.load(fdwi)
> data = img.get_data()
> affine = img.affine
>
> #free water
> fwdtimodel = fwdti.FreeWaterTensorModel(gtab, fit_method='NLS' )
> fwdtifit = fwdtimodel.fit(data, mask=mask)
> img = nib.Nifti1Image(fwdtifit.fa, affine)
> nib.save(img, join(dname, 'FWdti_FA.nii.gz'))
> img = nib.Nifti1Image(fwdtifit.md, affine)
> nib.save(img, join(dname, 'FWdti_MD.nii.gz'))
> img = nib.Nifti1Image(fwdtifit.ad, affine)
> nib.save(img, join(dname, 'FWdti_AD.nii.gz'))
> img = nib.Nifti1Image(fwdtifit.rd, affine)
> nib.save(img, join(dname, 'FWdti_RD.nii.gz'))
> img = nib.Nifti1Image(fwdtifit.f, affine)
> nib.save(img, join(dname, 'FWdti_fw.nii.gz'))
>
>
Where did `mask` come from?

Cheers,

Ariel

>
> On Fri, Jan 4, 2019 at 9:23 AM Ariel Rokem <arokem at gmail.com> wrote:
>
>> Hi Ping,
>>
>> I can't quite reproduce your error, though I am getting similar errors.
>> Could you also share the code that you are running?
>>
>> For the time being, the one thing that I noticed is that there are NaNs
>> in your data. That might be causing this issue.
>>
>> Cheers,
>>
>> Ariel
>>
>>
>>
>> On Mon, Dec 31, 2018 at 5:43 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>> wrote:
>>
>>> Hi Ariel,
>>>
>>>  Have you got the chance to look at the DWI data that was attached to
>>> the previous email?
>>>
>>> Thank you for your time.
>>>
>>> Ping
>>>
>>> On Sat, Dec 29, 2018 at 1:12 AM Ariel Rokem <arokem at gmail.com> wrote:
>>>
>>>> Hi Ping,
>>>>
>>>> Thanks for your email. Hard to say exactly what is going on without
>>>> further information. Could you tell us more about the data you are using?
>>>> How many b-values? How many directions? Any chance you could share the data
>>>> from the voxel that caused that error to be raised?
>>>>
>>>> Thanks!
>>>>
>>>> Ariel
>>>>
>>>> On Thu, Dec 27, 2018 at 6:55 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi Dipy Users,
>>>>>
>>>>>  I've ran into errors "Eigenvalues did not  converge" when using the
>>>>> free water elimination model,
>>>>> and here is the error message:
>>>>>
>>>>>   File
>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>>>> line 1615, in _decompose_tensor_nan
>>>>>     min_diffusivity=min_diffusivity)
>>>>>   File
>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>>>> line 1946, in decompose_tensor
>>>>>     eigenvals, eigenvecs = eigh(tensor)
>>>>>   File
>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/utils/arrfuncs.py",
>>>>> line 128, in eigh
>>>>>     return np.linalg.eigh(a, UPLO)
>>>>>   File
>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>>>> line 1291, in eigh
>>>>>     w, vt = gufunc(a, signature=signature, extobj=extobj)
>>>>>   File
>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>>>> line 95, in _raise_linalgerror_eigenvalues_nonconvergence
>>>>>     raise LinAlgError("Eigenvalues did not converge")
>>>>> numpy.linalg.linalg.LinAlgError: Eigenvalues did not converge
>>>>>
>>>>>
>>>>> Any suggestions?
>>>>>
>>>>> Thank you.
>>>>>
>>>>> Ping
>>>>>
>>>>> _______________________________________________
>>>>> Neuroimaging mailing list
>>>>> Neuroimaging at python.org
>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>
>>>> _______________________________________________
>>>> Neuroimaging mailing list
>>>> Neuroimaging at python.org
>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From markiewicz at stanford.edu  Fri Jan  4 12:29:26 2019
From: markiewicz at stanford.edu (Christopher Markiewicz)
Date: Fri, 4 Jan 2019 17:29:26 +0000
Subject: [Neuroimaging] Looping through 3D NIFTI Image: Help
In-Reply-To: <CA+NX+7pzOKp5oVQWKZ5LWVX66Eqdia-wKLVuX8ecU1uOoDmDng@mail.gmail.com>
References: <CA+NX+7pzOKp5oVQWKZ5LWVX66Eqdia-wKLVuX8ecU1uOoDmDng@mail.gmail.com>
Message-ID: <BN6PR02MB2675D6B8FF9A0E530F8CF072A98E0@BN6PR02MB2675.namprd02.prod.outlook.com>

Hi Arnav,


First, welcome! Just so you know, Neurostars (https://neurostars.org) is going to be a better place than StackOverflow to ask neuroscience/neuroinformatics questions. This list is also a good place, but I suspect Neurostars gets a wider audience.


Anyway, I'm interpreting your question as asking how to find the number of non-zero voxels in an image, multiplied by the voxel volume.


I would do it as follows:


-----


import numpy as np

import nibabel as nb

path = '...'
img = nb.load(path)

data = img.get_fdata(dtype=np.float32)

# Use a test that accounts for floating point imprecision; you may want a tighter threshold
non_zero_voxels = np.abs(data) > 1e-5


# NIfTI allows for non-mm spatial units

xyz_units = img.header.get_xyzt_units()[0]

factor = 1

if xyz_units == 'meter':

    factor = int(1e9)

elif xyz_units == 'micron':

    factor = 1e-9

# If missing, assume mm


# Voxel volume in mm^3

voxel_vol = np.prod(img.header.get_zooms()[:3]) * factor

non_zero_volume = non_zero_voxels.sum() * voxel_vol


-----


As a sanity check, human brains are generally around 1.5L, so if you're not seeing something on the order of 1-2 million mm^3, you might want to check on your data. If the numbers are off by more than a factor of 2 or so, you might have bad headers or your data might not be masked to 0 outside the brain.


For more information on working with nibabel images, I would highly recommend the documentation: http://nipy.org/nibabel/nibabel_images.html


Chris

________________________________
From: Neuroimaging <neuroimaging-bounces+markiewicz=stanford.edu at python.org> on behalf of Arnav Lohe <arnavlohe15 at gmail.com>
Sent: Friday, January 4, 2019 11:56:03 AM
To: neuroimaging at python.org
Subject: [Neuroimaging] Looping through 3D NIFTI Image: Help

Dear Neuroimaging List Members,

My name is Arnav Lohe, and I am a junior at Rutgers University working on a neuroimaging project. I want to write an original piece of code to calculate the total tissue volume in a (.nii) MRI image, and to do this I need to loop through the multidimensional array. The loop is what I do not know how to do. I tried triple indexing, I tried converting the .nii image into a numpy array, and got nowhere with my approaches. Does someone know how to loop through the individual voxels and extract the numerical information inside each one?

https://stackoverflow.com/questions/54031899/how-can-i-loop-through-3d-nifti-image-in-python

I have also posted this to StackOverflow, all additional relevant details should be there.

Sincerely,
Thanking you,
Arnav Lohe
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From markiewicz at stanford.edu  Fri Jan  4 13:40:21 2019
From: markiewicz at stanford.edu (Christopher Markiewicz)
Date: Fri, 4 Jan 2019 18:40:21 +0000
Subject: [Neuroimaging] ANN: nibabel 2.3.2
Message-ID: <BN6PR02MB26757276786100D946A109F4A98E0@BN6PR02MB2675.namprd02.prod.outlook.com>

Hi all,

Nibabel 2.3.2 was released this past Wednesday. 2.3.2 is a bug fix release, and it was primarily triggered by some API changes in the upcoming numpy 1.16.

Please cite using the Zenodo DOI: https://doi.org/10.5281/zenodo.2530243<https://doi.org/10.5281/zenodo.2530243>

Thanks to all contributors. This release also includes a number of fiddly fixes that improved the documentation and dealt with some of the accumulating warnings issued by upstream libraries, which is great for usability.

The full changelog follows:


Bug fix release for the 2.3 series.

Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke (MH)
Ben Cipollini (BC), Marc-Alexandre C?t? (MC), Chris Markiewicz (CM), Stephan
Gerhard (SG), Eric Larson (EL), Yaroslav Halchenko (YOH) and Chris Cheng (CC).

References like "pr/298" refer to github pull request numbers.

Enhancements
------------
* Enable toggling crosshair with ``Ctrl-x`` in ``OrthoSlicer3D`` viewer (pr/701)
  (Miguel Estevan Moreno, reviewed by CM)

Bug fixes
---------
* Read .PAR files corresponding to ADC maps (pr/685) (Gregory R. Lee, reviewed
  by CM)
* Increase maximum number of items read from Siemens CSA format (Igor Solovey,
  reviewed by CM, MB)
* Check boolean dtypes with ``numpy.issubdtype(..., np.bool_)`` (pr/707)
  (Jon Haitz Legarreta Gorro?o, reviewed by CM)

Maintenance
-----------
* Fix small typos in parrec2nii help text (pr/682) (Thomas Roos, reviewed by
  MB)
* Remove deprecated calls to ``numpy.asscalar`` (pr/686) (CM, reviewed by
  Gregory R. Lee)
* Update QA directives to accommodate Flake8 3.6 (pr/695) (CM)
* Update DOI links to use ``https://doi.org`` (pr/703) (Katrin Leinweber,
  reviewed by CM)
* Remove deprecated calls to ``numpy.fromstring`` (pr/700) (Ariel Rokem,
  reviewed by CM, MB)
* Drop ``distutils`` support, require ``bz2file`` for Python 2.7 (pr/700)
  (CM, reviewed by MB)
* Replace mutable ``bytes`` hack, disabled in numpy pre-release, with
  ``bytearray``/``readinto`` strategy (pr/700) (Ariel Rokem, CM, reviewed by
  CM, MB)

API changes and deprecations
----------------------------
* Add ``Opener.readinto`` method to read file contents into pre-allocated buffers
  (pr/700) (Ariel Rokem, reviewed by CM, MB)



--

Chris Markiewicz

Center for Reproducible Neuroscience

Stanford University
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From matthew.brett at gmail.com  Fri Jan  4 16:01:00 2019
From: matthew.brett at gmail.com (Matthew Brett)
Date: Fri, 4 Jan 2019 21:01:00 +0000
Subject: [Neuroimaging] ANN: nibabel 2.3.2
In-Reply-To: <BN6PR02MB26757276786100D946A109F4A98E0@BN6PR02MB2675.namprd02.prod.outlook.com>
References: <BN6PR02MB26757276786100D946A109F4A98E0@BN6PR02MB2675.namprd02.prod.outlook.com>
Message-ID: <CAH6Pt5oX=QERi00EEjGn3aeif7p5Jd6-_a7b_mhJdDtRQabmHg@mail.gmail.com>

Hi Chris,

On Fri, Jan 4, 2019 at 7:17 PM Christopher Markiewicz
<markiewicz at stanford.edu> wrote:
>
> Hi all,
>
> Nibabel 2.3.2 was released this past Wednesday. 2.3.2 is a bug fix release, and it was primarily triggered by some API changes in the upcoming numpy 1.16.
>
> Please cite using the Zenodo DOI: https://doi.org/10.5281/zenodo.2530243
>
> Thanks to all contributors. This release also includes a number of fiddly fixes that improved the documentation and dealt with some of the accumulating warnings issued by upstream libraries, which is great for usability.

Thanks very much for doing this release, and, as ever, doing all the hard work.

Cheers,

Matthew

From pinghongyeh at gmail.com  Fri Jan  4 13:31:35 2019
From: pinghongyeh at gmail.com (Ping-Hong Yeh)
Date: Fri, 4 Jan 2019 13:31:35 -0500
Subject: [Neuroimaging] failure using DIPY Free Water Elimination DTI
In-Reply-To: <CA+X4w0y921S3hRPQ7PMzTOBz-=Tw33xTojpQmqL0JkN6DnAj9g@mail.gmail.com>
References: <CAL1NnmNTd0z+k7-bu1+PSAk_zdcEdK2Yk+jPKAWzC0wt2CUCZA@mail.gmail.com>
 <CA+X4w0zE_wDfF3xFMBcT2ryhherw+esHOS4guhk98q614yT4AA@mail.gmail.com>
 <CAL1NnmMxoHER2vdvhTsk4TR2zMtanHfURx=+J-PxqwjTB9p1dw@mail.gmail.com>
 <CA+X4w0wDjWx3idaNyLjjpCwrnj8K7OD1oOS4ZGQTUHK71mxxNg@mail.gmail.com>
 <CAL1NnmMjJEMFgy20TqRc35egF3-w4GPDjLnW-DW_as61jTG5Bw@mail.gmail.com>
 <CA+X4w0y921S3hRPQ7PMzTOBz-=Tw33xTojpQmqL0JkN6DnAj9g@mail.gmail.com>
Message-ID: <CAL1NnmMDuSuqtx23HTUjep7FBewXUd=xf-z50i57GYyNgSL_BQ@mail.gmail.com>

I have attached the mask file.  Thank you.

maskimg = nib.load(join(dname, 'structural_mask.nii.gz'))
mask = maskimg.get_data()
affinemask = maskimg.affine


On Fri, Jan 4, 2019 at 1:13 PM Ariel Rokem <arokem at gmail.com> wrote:

>
> On Fri, Jan 4, 2019 at 7:42 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
> wrote:
>
>> Hi Ariel,
>>
>> Thank you for your time.
>>  I've run fslmaths using the syntax of -nan  beforehand, i thought that
>> has taken care of it.
>>
>
> I believe it's still there. My script crashed on that.
>
>
>> Here is the script i used,
>>
>> import dipy.reconst.fwdti as fwdti
>> Delta = 22.536
>> delta = 21.908
>> _Delta = 0.022536
>> _delta = 0.021908
>>
>> dname=os.path.join('/data/NEURO2/ping/MUX', id,
>> 'SOA_N270_plus19b0_fwd','data_DIFFPREP_t2acpc_proc_DRBUDDI_proc')
>> fdwi = join(dname,
>> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0_nan.nii.gz')
>> fbvec = join(dname,
>> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0_invY.bvecs') #the final
>> oriention after TORTOISE is RAS for earlier SOA289 data
>> fbval = join(dname,
>> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0.bvals')
>>
>> from dipy.io import read_bvals_bvecs
>> bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
>> from dipy.core.gradients import gradient_table
>> gtab = gradient_table(bvals, bvecs, big_delta=Delta, small_delta=delta)
>> img = nib.load(fdwi)
>> data = img.get_data()
>> affine = img.affine
>>
>> #free water
>> fwdtimodel = fwdti.FreeWaterTensorModel(gtab, fit_method='NLS' )
>> fwdtifit = fwdtimodel.fit(data, mask=mask)
>> img = nib.Nifti1Image(fwdtifit.fa, affine)
>> nib.save(img, join(dname, 'FWdti_FA.nii.gz'))
>> img = nib.Nifti1Image(fwdtifit.md, affine)
>> nib.save(img, join(dname, 'FWdti_MD.nii.gz'))
>> img = nib.Nifti1Image(fwdtifit.ad, affine)
>> nib.save(img, join(dname, 'FWdti_AD.nii.gz'))
>> img = nib.Nifti1Image(fwdtifit.rd, affine)
>> nib.save(img, join(dname, 'FWdti_RD.nii.gz'))
>> img = nib.Nifti1Image(fwdtifit.f, affine)
>> nib.save(img, join(dname, 'FWdti_fw.nii.gz'))
>>
>>
> Where did `mask` come from?
>
> Cheers,
>
> Ariel
>
>>
>> On Fri, Jan 4, 2019 at 9:23 AM Ariel Rokem <arokem at gmail.com> wrote:
>>
>>> Hi Ping,
>>>
>>> I can't quite reproduce your error, though I am getting similar errors.
>>> Could you also share the code that you are running?
>>>
>>> For the time being, the one thing that I noticed is that there are NaNs
>>> in your data. That might be causing this issue.
>>>
>>> Cheers,
>>>
>>> Ariel
>>>
>>>
>>>
>>> On Mon, Dec 31, 2018 at 5:43 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>>> wrote:
>>>
>>>> Hi Ariel,
>>>>
>>>>  Have you got the chance to look at the DWI data that was attached to
>>>> the previous email?
>>>>
>>>> Thank you for your time.
>>>>
>>>> Ping
>>>>
>>>> On Sat, Dec 29, 2018 at 1:12 AM Ariel Rokem <arokem at gmail.com> wrote:
>>>>
>>>>> Hi Ping,
>>>>>
>>>>> Thanks for your email. Hard to say exactly what is going on without
>>>>> further information. Could you tell us more about the data you are using?
>>>>> How many b-values? How many directions? Any chance you could share the data
>>>>> from the voxel that caused that error to be raised?
>>>>>
>>>>> Thanks!
>>>>>
>>>>> Ariel
>>>>>
>>>>> On Thu, Dec 27, 2018 at 6:55 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi Dipy Users,
>>>>>>
>>>>>>  I've ran into errors "Eigenvalues did not  converge" when using the
>>>>>> free water elimination model,
>>>>>> and here is the error message:
>>>>>>
>>>>>>   File
>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>>>>> line 1615, in _decompose_tensor_nan
>>>>>>     min_diffusivity=min_diffusivity)
>>>>>>   File
>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>>>>> line 1946, in decompose_tensor
>>>>>>     eigenvals, eigenvecs = eigh(tensor)
>>>>>>   File
>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/utils/arrfuncs.py",
>>>>>> line 128, in eigh
>>>>>>     return np.linalg.eigh(a, UPLO)
>>>>>>   File
>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>>>>> line 1291, in eigh
>>>>>>     w, vt = gufunc(a, signature=signature, extobj=extobj)
>>>>>>   File
>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>>>>> line 95, in _raise_linalgerror_eigenvalues_nonconvergence
>>>>>>     raise LinAlgError("Eigenvalues did not converge")
>>>>>> numpy.linalg.linalg.LinAlgError: Eigenvalues did not converge
>>>>>>
>>>>>>
>>>>>> Any suggestions?
>>>>>>
>>>>>> Thank you.
>>>>>>
>>>>>> Ping
>>>>>>
>>>>>> _______________________________________________
>>>>>> Neuroimaging mailing list
>>>>>> Neuroimaging at python.org
>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>
>>>>> _______________________________________________
>>>>> Neuroimaging mailing list
>>>>> Neuroimaging at python.org
>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>
>>>> _______________________________________________
>>>> Neuroimaging mailing list
>>>> Neuroimaging at python.org
>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From matthew.brett at gmail.com  Fri Jan  4 16:13:33 2019
From: matthew.brett at gmail.com (Matthew Brett)
Date: Fri, 4 Jan 2019 21:13:33 +0000
Subject: [Neuroimaging] Looping through 3D NIFTI Image: Help
In-Reply-To: <CA+NX+7pzOKp5oVQWKZ5LWVX66Eqdia-wKLVuX8ecU1uOoDmDng@mail.gmail.com>
References: <CA+NX+7pzOKp5oVQWKZ5LWVX66Eqdia-wKLVuX8ecU1uOoDmDng@mail.gmail.com>
Message-ID: <CAH6Pt5p41y_EUx_CzTBBkPkTK2ndmff1RcoHoBW7P0z+4DvuYQ@mail.gmail.com>

Hi,

On Fri, Jan 4, 2019 at 4:58 PM Arnav Lohe <arnavlohe15 at gmail.com> wrote:
>
> Dear Neuroimaging List Members,
>
> My name is Arnav Lohe, and I am a junior at Rutgers University working on a neuroimaging project. I want to write an original piece of code to calculate the total tissue volume in a (.nii) MRI image, and to do this I need to loop through the multidimensional array. The loop is what I do not know how to do. I tried triple indexing, I tried converting the .nii image into a numpy array, and got nowhere with my approaches. Does someone know how to loop through the individual voxels and extract the numerical information inside each one?

Just to add to other replies, it is almost always better to vectorize
- I mean - use Numpy arrays to do multiple operations at once.

For example, if your image is a grey matter probability image, and you
just want the sum of the voxels:

img = nib.load('my_image.nii')
data = img.get_fdata()
print(data.sum())

Or you want to do a histogram:

import matplotlib.pyplot as plt
plt.hist(data.ravel())

I don't myself do StackOverflow or Neurostars, so for nibabel
questions, at least, this list is a good place to ask.

Cheers,

Matthew

From skoudoro at iu.edu  Fri Jan  4 21:03:02 2019
From: skoudoro at iu.edu (Koudoro, Serge)
Date: Sat, 5 Jan 2019 02:03:02 +0000
Subject: [Neuroimaging] ANN: nibabel 2.3.2
In-Reply-To: <CAH6Pt5oX=QERi00EEjGn3aeif7p5Jd6-_a7b_mhJdDtRQabmHg@mail.gmail.com>
References: <BN6PR02MB26757276786100D946A109F4A98E0@BN6PR02MB2675.namprd02.prod.outlook.com>,
 <CAH6Pt5oX=QERi00EEjGn3aeif7p5Jd6-_a7b_mhJdDtRQabmHg@mail.gmail.com>
Message-ID: <1546653782333.72405@iu.edu>

Great!

Thanks to you and all devs for this release!

Serge K.
________________________________________
From: Neuroimaging <neuroimaging-bounces+skoudoro=iu.edu at python.org> on behalf of Matthew Brett <matthew.brett at gmail.com>
Sent: Friday, January 4, 2019 3:01 PM
To: Neuroimaging analysis in Python
Subject: Re: [Neuroimaging] ANN: nibabel 2.3.2

Hi Chris,

On Fri, Jan 4, 2019 at 7:17 PM Christopher Markiewicz
<markiewicz at stanford.edu> wrote:
>
> Hi all,
>
> Nibabel 2.3.2 was released this past Wednesday. 2.3.2 is a bug fix release, and it was primarily triggered by some API changes in the upcoming numpy 1.16.
>
> Please cite using the Zenodo DOI: https://doi.org/10.5281/zenodo.2530243
>
> Thanks to all contributors. This release also includes a number of fiddly fixes that improved the documentation and dealt with some of the accumulating warnings issued by upstream libraries, which is great for usability.

Thanks very much for doing this release, and, as ever, doing all the hard work.

Cheers,

Matthew
_______________________________________________
Neuroimaging mailing list
Neuroimaging at python.org
https://mail.python.org/mailman/listinfo/neuroimaging

From ts+ml at rcmd.org  Sun Jan  6 11:16:43 2019
From: ts+ml at rcmd.org (ts+ml at rcmd.org)
Date: Sun, 6 Jan 2019 17:16:43 +0100 (CET)
Subject: [Neuroimaging] Reading mgz files in NiBabel 2.3.0
Message-ID: <1897947400.183303.1546791404016@ox.hosteurope.de>

Dear list members,

I'm trying to load a FreeSurfer MGZ file (its header to be precise) using nibabel 2.3.0:

import nibabel.freesurfer.mghformat as fsmgh

def read_mgh(mgh_file_name):
    with open(mgh_file_name, 'rb') as mgh_file_handle:
        header = fsmgh.MGHHeader.from_fileobj(mgh_file_handle)
        ...

This works fine if the file is in MGH format, but NOT if it is gzipped (MGZ format). In that case, you get the following exception in the last line:

klass = <class 'nibabel.freesurfer.mghformat.MGHHeader'>, fileobj = <closed file '/home/spirit/develop/brainload/tests/brainload/../test_data/subject1/mri/orig.mgz', mode 'rb' at 0x7f2448ef2e40>
check = True

    @classmethod
    def from_fileobj(klass, fileobj, check=True):
        '''
            classmethod for loading a MGH fileobject
            '''
        # We need the following hack because MGH data stores header information
        # after the data chunk too. We read the header initially, deduce the
        # dimensions from the header, skip over and then read the footer
        # information
        hdr_str = fileobj.read(klass._hdrdtype.itemsize)
        hdr_str_to_np = np.ndarray(shape=(), dtype=klass._hdrdtype,
                                   buffer=hdr_str)
        if not np.all(hdr_str_to_np['dims']):
>           raise MGHError('Dimensions of the data should be non-zero')
E           MGHError: Dimensions of the data should be non-zero

env/local/lib/python2.7/site-packages/nibabel/freesurfer/mghformat.py:165: MGHError



So my question is: how should I read the file? Am I supposed to unpack it myself before reading, or is there some other function for this in nibabel which I overlooked?

The files in question are available here in case you want them:
- The MGZ file, it fails with this one: http://rcmd.org/tmp/orig.mgz
- The same file, manually unzipped using gunzip in the shell. The code works with this one: http://rcmd.org/tmp/orig.mgh


Thanks in advance,

-- 
Tim

From arokem at gmail.com  Mon Jan  7 22:48:35 2019
From: arokem at gmail.com (Ariel Rokem)
Date: Mon, 7 Jan 2019 19:48:35 -0800
Subject: [Neuroimaging] NeuroHackademy 2019
Message-ID: <CA+X4w0wci4Azq1z2iT1Jb51-7=aRBOqMr5VU3wWgLsbojcZ=2Q@mail.gmail.com>

We are happy to announce a call for applications to participate in
Neurohackademy 2019!

This two-week hands-on workshop held at the University of Washington
eScience Institute in Seattle, July 29th - August 9th, 2019, focuses on
tools and techniques used to analyze human neuroscience data, on methods
used to extract information from large datasets of publicly available data
(such as the Human Connectome Project, OpenfMRI, etc.), and on tools for
making human neuroscience research open and reproducible.

Neurohackademy sessions in the first week will include lectures and
tutorials on data science, machine learning, data visualization and data
resources. The second week will be devoted to participant-directed
activities: guided work on team projects, hackathon sessions, and breakout
sessions on topics of interest.

*For more details and a preliminary list of instructors, see:
**https://neurohackademy.org/
<https://neurohackademy.org/>*

We are now accepting applications to participate at:
https://neurohackademy.org/apply/

Ideally, applicants should have some prior experience with programming and
with neuroscience data analysis, but we welcome applications from
participants with a variety of relevant backgrounds.

Accepted applicants will be asked to pay a fee of $200 upon final
registration. This fee will include participation in the course,
accommodation in the UW dorms, and two meals a day (breakfast and lunch),
for the duration of the course. A limited number of fee waivers and travel
grants will be available. We encourage students with financial need and
students from groups that are underrepresented in neuroimaging and data
science to apply for these grants (see application form for details).

*Important dates:*
*February 18th: Application deadline*
*March 15th: Notification of acceptance*
*April 1st: Final registration deadline*

On behalf of the instructors,

Ariel Rokem, University of Washington
Tal Yarkoni, University of Texas, Austin
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From bakk.hbg at googlemail.com  Tue Jan  8 12:30:22 2019
From: bakk.hbg at googlemail.com (Barbara Kreilkamp)
Date: Tue, 8 Jan 2019 17:30:22 +0000
Subject: [Neuroimaging] Postdoctoral Position: structural/functional
 connectivity and networks
Message-ID: <12747630-429a-9c90-80ed-270da5a96bd5@googlemail.com>

Dear all,

As a current post-doc in this lab, I am happy to announce this 
three-year post-doc opportunity availabile in Dr Simon Keller's lab at 
the University of Liverpool, United Kingdom.

The successful applicant will be specialising in structural and 
functional brain connectivity and networks in human epilepsy. Please 
find more information here 
https://www.jobs.ac.uk/job/BPF608/postdoctoral-research-fellow-neuroimaging-grade-7?and 
in this PDF https://app.box.com/s/8tiylekoiivq4s3kx8fmlsotply8kd0h

Please read this job description and direct your informal inquiries to 
Dr Simon Keller (simon.keller at liv.ac.uk <mailto:simon.keller at liv.ac.uk>).

Kind regards and a happy new year!
Barbara
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From ts+ml at rcmd.org  Wed Jan  9 03:45:25 2019
From: ts+ml at rcmd.org (ts+ml at rcmd.org)
Date: Wed, 9 Jan 2019 09:45:25 +0100 (CET)
Subject: [Neuroimaging] Reading mgz files in NiBabel 2.3.0
In-Reply-To: <1897947400.183303.1546791404016@ox.hosteurope.de>
References: <1897947400.183303.1546791404016@ox.hosteurope.de>
Message-ID: <1684110950.190435.1547023525736@ox.hosteurope.de>

I must have been very confused when I wrote that, sorry. Of course, the question doesn't make much sense as the nibabel function gets the file handle only. One should just gzip.open() in case the file name end with 'mgz' I guess. Sorry for the noise.


> On January 6, 2019 at 5:16 PM ts+ml at rcmd.org wrote:
> 
> 
> Dear list members,
> 
> I'm trying to load a FreeSurfer MGZ file (its header to be precise) using nibabel 2.3.0:

-- 
Tim

From pinghongyeh at gmail.com  Wed Jan  9 07:47:03 2019
From: pinghongyeh at gmail.com (Ping-Hong Yeh)
Date: Wed, 9 Jan 2019 07:47:03 -0500
Subject: [Neuroimaging] failure using DIPY Free Water Elimination DTI
In-Reply-To: <CAL1NnmMDuSuqtx23HTUjep7FBewXUd=xf-z50i57GYyNgSL_BQ@mail.gmail.com>
References: <CAL1NnmNTd0z+k7-bu1+PSAk_zdcEdK2Yk+jPKAWzC0wt2CUCZA@mail.gmail.com>
 <CA+X4w0zE_wDfF3xFMBcT2ryhherw+esHOS4guhk98q614yT4AA@mail.gmail.com>
 <CAL1NnmMxoHER2vdvhTsk4TR2zMtanHfURx=+J-PxqwjTB9p1dw@mail.gmail.com>
 <CA+X4w0wDjWx3idaNyLjjpCwrnj8K7OD1oOS4ZGQTUHK71mxxNg@mail.gmail.com>
 <CAL1NnmMjJEMFgy20TqRc35egF3-w4GPDjLnW-DW_as61jTG5Bw@mail.gmail.com>
 <CA+X4w0y921S3hRPQ7PMzTOBz-=Tw33xTojpQmqL0JkN6DnAj9g@mail.gmail.com>
 <CAL1NnmMDuSuqtx23HTUjep7FBewXUd=xf-z50i57GYyNgSL_BQ@mail.gmail.com>
Message-ID: <CAL1NnmMk+3T-XMYr9eoT6j5fu83GGkY7cyS0Et4pzGRbjFJU9w@mail.gmail.com>

Hi Ariel

Have you got the mask file?

Any update?

Thanks!
Ping

On Fri, Jan 4, 2019 at 1:31 PM Ping-Hong Yeh <pinghongyeh at gmail.com> wrote:

> I have attached the mask file.  Thank you.
>
> maskimg = nib.load(join(dname, 'structural_mask.nii.gz'))
> mask = maskimg.get_data()
> affinemask = maskimg.affine
>
>
> On Fri, Jan 4, 2019 at 1:13 PM Ariel Rokem <arokem at gmail.com> wrote:
>
>>
>> On Fri, Jan 4, 2019 at 7:42 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>> wrote:
>>
>>> Hi Ariel,
>>>
>>> Thank you for your time.
>>>  I've run fslmaths using the syntax of -nan  beforehand, i thought that
>>> has taken care of it.
>>>
>>
>> I believe it's still there. My script crashed on that.
>>
>>
>>> Here is the script i used,
>>>
>>> import dipy.reconst.fwdti as fwdti
>>> Delta = 22.536
>>> delta = 21.908
>>> _Delta = 0.022536
>>> _delta = 0.021908
>>>
>>> dname=os.path.join('/data/NEURO2/ping/MUX', id,
>>> 'SOA_N270_plus19b0_fwd','data_DIFFPREP_t2acpc_proc_DRBUDDI_proc')
>>> fdwi = join(dname,
>>> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0_nan.nii.gz')
>>> fbvec = join(dname,
>>> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0_invY.bvecs') #the final
>>> oriention after TORTOISE is RAS for earlier SOA289 data
>>> fbval = join(dname,
>>> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0.bvals')
>>>
>>> from dipy.io import read_bvals_bvecs
>>> bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
>>> from dipy.core.gradients import gradient_table
>>> gtab = gradient_table(bvals, bvecs, big_delta=Delta, small_delta=delta)
>>> img = nib.load(fdwi)
>>> data = img.get_data()
>>> affine = img.affine
>>>
>>> #free water
>>> fwdtimodel = fwdti.FreeWaterTensorModel(gtab, fit_method='NLS' )
>>> fwdtifit = fwdtimodel.fit(data, mask=mask)
>>> img = nib.Nifti1Image(fwdtifit.fa, affine)
>>> nib.save(img, join(dname, 'FWdti_FA.nii.gz'))
>>> img = nib.Nifti1Image(fwdtifit.md, affine)
>>> nib.save(img, join(dname, 'FWdti_MD.nii.gz'))
>>> img = nib.Nifti1Image(fwdtifit.ad, affine)
>>> nib.save(img, join(dname, 'FWdti_AD.nii.gz'))
>>> img = nib.Nifti1Image(fwdtifit.rd, affine)
>>> nib.save(img, join(dname, 'FWdti_RD.nii.gz'))
>>> img = nib.Nifti1Image(fwdtifit.f, affine)
>>> nib.save(img, join(dname, 'FWdti_fw.nii.gz'))
>>>
>>>
>> Where did `mask` come from?
>>
>> Cheers,
>>
>> Ariel
>>
>>>
>>> On Fri, Jan 4, 2019 at 9:23 AM Ariel Rokem <arokem at gmail.com> wrote:
>>>
>>>> Hi Ping,
>>>>
>>>> I can't quite reproduce your error, though I am getting similar errors.
>>>> Could you also share the code that you are running?
>>>>
>>>> For the time being, the one thing that I noticed is that there are NaNs
>>>> in your data. That might be causing this issue.
>>>>
>>>> Cheers,
>>>>
>>>> Ariel
>>>>
>>>>
>>>>
>>>> On Mon, Dec 31, 2018 at 5:43 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi Ariel,
>>>>>
>>>>>  Have you got the chance to look at the DWI data that was attached to
>>>>> the previous email?
>>>>>
>>>>> Thank you for your time.
>>>>>
>>>>> Ping
>>>>>
>>>>> On Sat, Dec 29, 2018 at 1:12 AM Ariel Rokem <arokem at gmail.com> wrote:
>>>>>
>>>>>> Hi Ping,
>>>>>>
>>>>>> Thanks for your email. Hard to say exactly what is going on without
>>>>>> further information. Could you tell us more about the data you are using?
>>>>>> How many b-values? How many directions? Any chance you could share the data
>>>>>> from the voxel that caused that error to be raised?
>>>>>>
>>>>>> Thanks!
>>>>>>
>>>>>> Ariel
>>>>>>
>>>>>> On Thu, Dec 27, 2018 at 6:55 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Dipy Users,
>>>>>>>
>>>>>>>  I've ran into errors "Eigenvalues did not  converge" when using the
>>>>>>> free water elimination model,
>>>>>>> and here is the error message:
>>>>>>>
>>>>>>>   File
>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>>>>>> line 1615, in _decompose_tensor_nan
>>>>>>>     min_diffusivity=min_diffusivity)
>>>>>>>   File
>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>>>>>> line 1946, in decompose_tensor
>>>>>>>     eigenvals, eigenvecs = eigh(tensor)
>>>>>>>   File
>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/utils/arrfuncs.py",
>>>>>>> line 128, in eigh
>>>>>>>     return np.linalg.eigh(a, UPLO)
>>>>>>>   File
>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>>>>>> line 1291, in eigh
>>>>>>>     w, vt = gufunc(a, signature=signature, extobj=extobj)
>>>>>>>   File
>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>>>>>> line 95, in _raise_linalgerror_eigenvalues_nonconvergence
>>>>>>>     raise LinAlgError("Eigenvalues did not converge")
>>>>>>> numpy.linalg.linalg.LinAlgError: Eigenvalues did not converge
>>>>>>>
>>>>>>>
>>>>>>> Any suggestions?
>>>>>>>
>>>>>>> Thank you.
>>>>>>>
>>>>>>> Ping
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Neuroimaging mailing list
>>>>>>> Neuroimaging at python.org
>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>
>>>>>> _______________________________________________
>>>>>> Neuroimaging mailing list
>>>>>> Neuroimaging at python.org
>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>
>>>>> _______________________________________________
>>>>> Neuroimaging mailing list
>>>>> Neuroimaging at python.org
>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>
>>>> _______________________________________________
>>>> Neuroimaging mailing list
>>>> Neuroimaging at python.org
>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>
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From alexandra.badea at duke.edu  Wed Jan  9 11:45:21 2019
From: alexandra.badea at duke.edu (Alexandra Badea, Ph.D.)
Date: Wed, 9 Jan 2019 16:45:21 +0000
Subject: [Neuroimaging] metrics on bundles in dipy
Message-ID: <86C83DD5-BCA9-41B5-BD77-F13DAE9D3FE7@duke.edu>

Hi!
I am trying to use dipy to extract image associated metrics like FA on bundles. I guess this has already been implemented, and would be grateful for a pointer to the proper function.
Alternatively, will try and write a script to interpolate values from images to bundle centroids.
Many thanks,
Alexandra
-

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From arokem at gmail.com  Thu Jan 10 13:48:50 2019
From: arokem at gmail.com (Ariel Rokem)
Date: Thu, 10 Jan 2019 10:48:50 -0800
Subject: [Neuroimaging] metrics on bundles in dipy
In-Reply-To: <86C83DD5-BCA9-41B5-BD77-F13DAE9D3FE7@duke.edu>
References: <86C83DD5-BCA9-41B5-BD77-F13DAE9D3FE7@duke.edu>
Message-ID: <CA+X4w0x=yEnMY-RgphnTtR-14vJNvmxMA82bwmROdpwr8u0Y6w@mail.gmail.com>

Hi Alexandra,

There's a work-in-progress pull request implementing something like this:
https://github.com/nipy/dipy/pull/1695

For the time being, you'll need to pull this branch down to get these
features, but it should make it into the master branch soon, and hopefully
into the next release.

Cheers,

Ariel

On Wed, Jan 9, 2019 at 8:45 AM Alexandra Badea, Ph.D. <
alexandra.badea at duke.edu> wrote:

> Hi!
>
> I am trying to use dipy to extract image associated metrics like FA on
> bundles. I guess this has already been implemented, and would be grateful
> for a pointer to the proper function.
>
> Alternatively, will try and write a script to interpolate values from
> images to bundle centroids.
>
> Many thanks,
>
> Alexandra
>
> -
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From alexandra.badea at duke.edu  Thu Jan 10 14:04:05 2019
From: alexandra.badea at duke.edu (Alexandra Badea, Ph.D.)
Date: Thu, 10 Jan 2019 19:04:05 +0000
Subject: [Neuroimaging] metrics on bundles in dipy
In-Reply-To: <CA+X4w0x=yEnMY-RgphnTtR-14vJNvmxMA82bwmROdpwr8u0Y6w@mail.gmail.com>
References: <86C83DD5-BCA9-41B5-BD77-F13DAE9D3FE7@duke.edu>
 <CA+X4w0x=yEnMY-RgphnTtR-14vJNvmxMA82bwmROdpwr8u0Y6w@mail.gmail.com>
Message-ID: <89FC9939-C0D3-479B-8CDC-B382BA5F0934@duke.edu>

Great news, thanks much Ariel!

Alexandra


From: Neuroimaging <neuroimaging-bounces+alexandra.badea=duke.edu at python.org> on behalf of Ariel Rokem <arokem at gmail.com>
Reply-To: Neuroimaging analysis in Python <neuroimaging at python.org>
Date: Thursday, January 10, 2019 at 1:48 PM
To: Neuroimaging analysis in Python <neuroimaging at python.org>
Subject: Re: [Neuroimaging] metrics on bundles in dipy

Hi Alexandra,

There's a work-in-progress pull request implementing something like this: https://github.com/nipy/dipy/pull/1695<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_nipy_dipy_pull_1695&d=DwMFaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=UQt1LXgkyi1oV3SGw0TEAX3QuV3b_wY3ZLvHmk-zBkg&m=e8XSvuBxwvDrvmUBn-J3jnIE9vqaPGBVRgWEBmTB_pA&s=pSq9E_q-sixc2rROc5WNiUncj-6D9UtRXcjt349zF6o&e=>

For the time being, you'll need to pull this branch down to get these features, but it should make it into the master branch soon, and hopefully into the next release.

Cheers,

Ariel

On Wed, Jan 9, 2019 at 8:45 AM Alexandra Badea, Ph.D. <alexandra.badea at duke.edu<mailto:alexandra.badea at duke.edu>> wrote:
Hi!
I am trying to use dipy to extract image associated metrics like FA on bundles. I guess this has already been implemented, and would be grateful for a pointer to the proper function.
Alternatively, will try and write a script to interpolate values from images to bundle centroids.
Many thanks,
Alexandra
-

_______________________________________________
Neuroimaging mailing list
Neuroimaging at python.org<mailto:Neuroimaging at python.org>
https://mail.python.org/mailman/listinfo/neuroimaging<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.python.org_mailman_listinfo_neuroimaging&d=DwMFaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=UQt1LXgkyi1oV3SGw0TEAX3QuV3b_wY3ZLvHmk-zBkg&m=e8XSvuBxwvDrvmUBn-J3jnIE9vqaPGBVRgWEBmTB_pA&s=ZuO6bfAIXAFESzhTMqHoe_KlPtMuyeqLrrRZt8zCs6U&e=>
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From arokem at gmail.com  Thu Jan 10 18:27:29 2019
From: arokem at gmail.com (Ariel Rokem)
Date: Thu, 10 Jan 2019 15:27:29 -0800
Subject: [Neuroimaging] failure using DIPY Free Water Elimination DTI
In-Reply-To: <CAL1NnmMk+3T-XMYr9eoT6j5fu83GGkY7cyS0Et4pzGRbjFJU9w@mail.gmail.com>
References: <CAL1NnmNTd0z+k7-bu1+PSAk_zdcEdK2Yk+jPKAWzC0wt2CUCZA@mail.gmail.com>
 <CA+X4w0zE_wDfF3xFMBcT2ryhherw+esHOS4guhk98q614yT4AA@mail.gmail.com>
 <CAL1NnmMxoHER2vdvhTsk4TR2zMtanHfURx=+J-PxqwjTB9p1dw@mail.gmail.com>
 <CA+X4w0wDjWx3idaNyLjjpCwrnj8K7OD1oOS4ZGQTUHK71mxxNg@mail.gmail.com>
 <CAL1NnmMjJEMFgy20TqRc35egF3-w4GPDjLnW-DW_as61jTG5Bw@mail.gmail.com>
 <CA+X4w0y921S3hRPQ7PMzTOBz-=Tw33xTojpQmqL0JkN6DnAj9g@mail.gmail.com>
 <CAL1NnmMDuSuqtx23HTUjep7FBewXUd=xf-z50i57GYyNgSL_BQ@mail.gmail.com>
 <CAL1NnmMk+3T-XMYr9eoT6j5fu83GGkY7cyS0Et4pzGRbjFJU9w@mail.gmail.com>
Message-ID: <CA+X4w0yD6QMOc=h4qNnRVcwkwaT7rZHvMT2KdJDjU3xhBT8pMg@mail.gmail.com>

Hi Ping,

Sorry. Using your mask, I can't reproduce the error. Here is my code:
https://gist.github.com/arokem/2b7963ad5bd625f24e60c4a9307e7b7c

I'd make sure to get rid of all the nans first (although I didn't seem to
need to do this in my implementation).

Hope that helps,

Ariel

On Wed, Jan 9, 2019 at 4:47 AM Ping-Hong Yeh <pinghongyeh at gmail.com> wrote:

> Hi Ariel
>
> Have you got the mask file?
>
> Any update?
>
> Thanks!
> Ping
>
> On Fri, Jan 4, 2019 at 1:31 PM Ping-Hong Yeh <pinghongyeh at gmail.com>
> wrote:
>
>> I have attached the mask file.  Thank you.
>>
>> maskimg = nib.load(join(dname, 'structural_mask.nii.gz'))
>> mask = maskimg.get_data()
>> affinemask = maskimg.affine
>>
>>
>> On Fri, Jan 4, 2019 at 1:13 PM Ariel Rokem <arokem at gmail.com> wrote:
>>
>>>
>>> On Fri, Jan 4, 2019 at 7:42 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>>> wrote:
>>>
>>>> Hi Ariel,
>>>>
>>>> Thank you for your time.
>>>>  I've run fslmaths using the syntax of -nan  beforehand, i thought that
>>>> has taken care of it.
>>>>
>>>
>>> I believe it's still there. My script crashed on that.
>>>
>>>
>>>> Here is the script i used,
>>>>
>>>> import dipy.reconst.fwdti as fwdti
>>>> Delta = 22.536
>>>> delta = 21.908
>>>> _Delta = 0.022536
>>>> _delta = 0.021908
>>>>
>>>> dname=os.path.join('/data/NEURO2/ping/MUX', id,
>>>> 'SOA_N270_plus19b0_fwd','data_DIFFPREP_t2acpc_proc_DRBUDDI_proc')
>>>> fdwi = join(dname,
>>>> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0_nan.nii.gz')
>>>> fbvec = join(dname,
>>>> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0_invY.bvecs') #the final
>>>> oriention after TORTOISE is RAS for earlier SOA289 data
>>>> fbval = join(dname,
>>>> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0.bvals')
>>>>
>>>> from dipy.io import read_bvals_bvecs
>>>> bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
>>>> from dipy.core.gradients import gradient_table
>>>> gtab = gradient_table(bvals, bvecs, big_delta=Delta, small_delta=delta)
>>>> img = nib.load(fdwi)
>>>> data = img.get_data()
>>>> affine = img.affine
>>>>
>>>> #free water
>>>> fwdtimodel = fwdti.FreeWaterTensorModel(gtab, fit_method='NLS' )
>>>> fwdtifit = fwdtimodel.fit(data, mask=mask)
>>>> img = nib.Nifti1Image(fwdtifit.fa, affine)
>>>> nib.save(img, join(dname, 'FWdti_FA.nii.gz'))
>>>> img = nib.Nifti1Image(fwdtifit.md, affine)
>>>> nib.save(img, join(dname, 'FWdti_MD.nii.gz'))
>>>> img = nib.Nifti1Image(fwdtifit.ad, affine)
>>>> nib.save(img, join(dname, 'FWdti_AD.nii.gz'))
>>>> img = nib.Nifti1Image(fwdtifit.rd, affine)
>>>> nib.save(img, join(dname, 'FWdti_RD.nii.gz'))
>>>> img = nib.Nifti1Image(fwdtifit.f, affine)
>>>> nib.save(img, join(dname, 'FWdti_fw.nii.gz'))
>>>>
>>>>
>>> Where did `mask` come from?
>>>
>>> Cheers,
>>>
>>> Ariel
>>>
>>>>
>>>> On Fri, Jan 4, 2019 at 9:23 AM Ariel Rokem <arokem at gmail.com> wrote:
>>>>
>>>>> Hi Ping,
>>>>>
>>>>> I can't quite reproduce your error, though I am getting similar
>>>>> errors. Could you also share the code that you are running?
>>>>>
>>>>> For the time being, the one thing that I noticed is that there are
>>>>> NaNs in your data. That might be causing this issue.
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Ariel
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Dec 31, 2018 at 5:43 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi Ariel,
>>>>>>
>>>>>>  Have you got the chance to look at the DWI data that was attached to
>>>>>> the previous email?
>>>>>>
>>>>>> Thank you for your time.
>>>>>>
>>>>>> Ping
>>>>>>
>>>>>> On Sat, Dec 29, 2018 at 1:12 AM Ariel Rokem <arokem at gmail.com> wrote:
>>>>>>
>>>>>>> Hi Ping,
>>>>>>>
>>>>>>> Thanks for your email. Hard to say exactly what is going on without
>>>>>>> further information. Could you tell us more about the data you are using?
>>>>>>> How many b-values? How many directions? Any chance you could share the data
>>>>>>> from the voxel that caused that error to be raised?
>>>>>>>
>>>>>>> Thanks!
>>>>>>>
>>>>>>> Ariel
>>>>>>>
>>>>>>> On Thu, Dec 27, 2018 at 6:55 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi Dipy Users,
>>>>>>>>
>>>>>>>>  I've ran into errors "Eigenvalues did not  converge" when using
>>>>>>>> the free water elimination model,
>>>>>>>> and here is the error message:
>>>>>>>>
>>>>>>>>   File
>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>>>>>>> line 1615, in _decompose_tensor_nan
>>>>>>>>     min_diffusivity=min_diffusivity)
>>>>>>>>   File
>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>>>>>>> line 1946, in decompose_tensor
>>>>>>>>     eigenvals, eigenvecs = eigh(tensor)
>>>>>>>>   File
>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/utils/arrfuncs.py",
>>>>>>>> line 128, in eigh
>>>>>>>>     return np.linalg.eigh(a, UPLO)
>>>>>>>>   File
>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>>>>>>> line 1291, in eigh
>>>>>>>>     w, vt = gufunc(a, signature=signature, extobj=extobj)
>>>>>>>>   File
>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>>>>>>> line 95, in _raise_linalgerror_eigenvalues_nonconvergence
>>>>>>>>     raise LinAlgError("Eigenvalues did not converge")
>>>>>>>> numpy.linalg.linalg.LinAlgError: Eigenvalues did not converge
>>>>>>>>
>>>>>>>>
>>>>>>>> Any suggestions?
>>>>>>>>
>>>>>>>> Thank you.
>>>>>>>>
>>>>>>>> Ping
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Neuroimaging mailing list
>>>>>>>> Neuroimaging at python.org
>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Neuroimaging mailing list
>>>>>>> Neuroimaging at python.org
>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>
>>>>>> _______________________________________________
>>>>>> Neuroimaging mailing list
>>>>>> Neuroimaging at python.org
>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>
>>>>> _______________________________________________
>>>>> Neuroimaging mailing list
>>>>> Neuroimaging at python.org
>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>
>>>> _______________________________________________
>>>> Neuroimaging mailing list
>>>> Neuroimaging at python.org
>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From eric.condamine at univ-grenoble-alpes.fr  Fri Jan 11 10:26:05 2019
From: eric.condamine at univ-grenoble-alpes.fr (Eric Condamine)
Date: Fri, 11 Jan 2019 16:26:05 +0100
Subject: [Neuroimaging] Apply resolution of one image.nii to another
 image.nii
Message-ID: <aadb5f63-7d14-dc73-251d-3b32e479c9e7@univ-grenoble-alpes.fr>

Hello nipy experts,
I would like to change the resolution of an nifti image (let's say 
mask.nii) according to the resolution of one other nifti image (let's 
say ref.nii), a process that i was doing with the imcalc function of spm 
before i start to switch to python ... i confess that i do not yet know 
all the tools currently available under nipy umbrella ...
One way to do it could be something like that.

"""
from skimage.transform import resize
import nibabel as nib

mask = nib.load(mask.nii)
mask_data = mask.get_fdata()

ref = nib.load(ref.nii)
ref_data = ref.get_fdata()

ref_size = ref_data.shape[:3]
resized_mask_data = resize(mask_data, ref_size, order=1, mode='reflect') 
# order=1 (Bi-linear) is the default value and it seems that with 3D 
image, Bi-linear is equivalent to 'trilinear' of SPM's imcalc function ?

mask_final = nib.Nifti1Image(resized_mask_data, xxx, yyy)
nib.save(mask_final, mask_final)

I do not succeed to obtain the wanted mask_final.nii (exactly the same 
as mask.nii, ie. same orientation in the same space, with only a change 
of the resolution). may be I am wrong with the xxx and yyy in 
nib.Nifti1Image().

I tried:
nib.Nifti1Image(resized_mask_data, mask.affine, ref.header)
or
nib.Nifti1Image(resized_mask_data, mask.affine, mask.header)
etc. without success.

So I plan to make a python function in order to make the correct header 
for the mask_final.nii after the resize() function.

Because this need seems pretty commun, i guess that a tools to do it is 
is already existing in python ?

So before reinvent the wheel, I would like to be sure that I do not make 
mistake with? xxx and/or yyy ?

May be other function/tool doing the job and that I do not know exist ?

Thank you for all suggests or informations,

All the best.
-- 

Eric Condamine  <http://fr.linkedin.com/pub/eric-condamine/27/529/290>

IRMaGe  <https://irmage.ujf-grenoble.fr/>
INSERM US17-CNRS UMS3552-UGA-CHUGA
Unit? IRM 3T Recherche
CHU Grenoble - CS 10217
38043 Grenoble Cedex 9

Tel : (00 33) 4 7676 7575 - Poste 63 202
     : (00 33) 4 7676 8726
Fax : (00 33) 4 7676 9305
e-mail:eric.condamine at univ-grenoble-alpes.fr  <eric.condamine at univ-grenoble-alpes.f>

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From matthew.brett at gmail.com  Fri Jan 11 11:00:12 2019
From: matthew.brett at gmail.com (Matthew Brett)
Date: Fri, 11 Jan 2019 16:00:12 +0000
Subject: [Neuroimaging] Apply resolution of one image.nii to another
 image.nii
In-Reply-To: <aadb5f63-7d14-dc73-251d-3b32e479c9e7@univ-grenoble-alpes.fr>
References: <aadb5f63-7d14-dc73-251d-3b32e479c9e7@univ-grenoble-alpes.fr>
Message-ID: <CAH6Pt5paJru9=XrUkH31tpN+zu9JqBD2Eb8xoR2urJdFn988Sg@mail.gmail.com>

Hi,


On Fri, Jan 11, 2019 at 3:26 PM Eric Condamine
<eric.condamine at univ-grenoble-alpes.fr> wrote:
>
> Hello nipy experts,
> I would like to change the resolution of an nifti image (let's say mask.nii) according to the resolution of one other nifti image (let's say ref.nii), a process that i was doing with the imcalc function of spm before i start to switch to python ... i confess that i do not yet know all the tools currently available under nipy umbrella ...
> One way to do it could be something like that.
>
> """
> from skimage.transform import resize
> import nibabel as nib
>
> mask = nib.load(mask.nii)
> mask_data = mask.get_fdata()
>
> ref = nib.load(ref.nii)
> ref_data = ref.get_fdata()
>
> ref_size = ref_data.shape[:3]
> resized_mask_data = resize(mask_data, ref_size, order=1, mode='reflect') # order=1 (Bi-linear) is the default value and it seems that with 3D image, Bi-linear is equivalent to 'trilinear' of SPM's imcalc function ?

Did you discover the processing module in nibabel?

Maybe "resample_from_to" would help:

http://nipy.org/nibabel/reference/nibabel.processing.html#nibabel.processing.resample_from_to

Something like:

import nibabel.processing as nibp
resized = nibp.resample_from_to(mask, ref)

Does that work?  You'd probably have to threshold the image binarize
it - trilinear resampling is the default - or use 0 (nearest neighbor)
resampling.

Cheers,

Matthew

From diana.prata at kcl.ac.uk  Fri Jan 11 20:26:37 2019
From: diana.prata at kcl.ac.uk (Prata, Diana)
Date: Sat, 12 Jan 2019 01:26:37 +0000
Subject: [Neuroimaging] TWO POST-DOC POSITIONS IN NEUROIMAGING @LISBON
Message-ID: <C0D1ECE3-29E3-4F70-96F6-91A6FA270A0A@kcl.ac.uk>

TWO POST-DOC POSITIONS IN NEUROIMAGING @LISBON

Two post-doc vacancies opened at the Biomedical Neuroscience Lab (https://dpratalab.wordpress.com/; PI: Dr Diana Prata, with double affiliation in King?s College London), at the University of Lisbon - for research in human social neuroscience and the oxytocin and the dopamine systems in a highly interdisciplinary 3-year project involving pharmacology, genetics and a range of psychophysiological techniques. Expertise in fMRI and/or EEG highly preferred; and in eye-tracking and SCR favourable. Negotiable salary. Open until 26th of Jan 2019. We look forward to welcoming you!: http://www.eracareers.pt/opportunities/index.aspx?task=global&jobId=106526


Diana Prata, Phd
Marie Curie Fellow
Principal Investigator (Biomedical Neuroscience Lab), Instituto de Biof?sica e Engenharia Biom?dica, FCUL
Visiting Lecturer, IoPPN, King's College London

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From pinghongyeh at gmail.com  Sat Jan 12 16:17:05 2019
From: pinghongyeh at gmail.com (Ping-Hong Yeh)
Date: Sat, 12 Jan 2019 16:17:05 -0500
Subject: [Neuroimaging] failure using DIPY Free Water Elimination DTI
In-Reply-To: <CA+X4w0yD6QMOc=h4qNnRVcwkwaT7rZHvMT2KdJDjU3xhBT8pMg@mail.gmail.com>
References: <CAL1NnmNTd0z+k7-bu1+PSAk_zdcEdK2Yk+jPKAWzC0wt2CUCZA@mail.gmail.com>
 <CA+X4w0zE_wDfF3xFMBcT2ryhherw+esHOS4guhk98q614yT4AA@mail.gmail.com>
 <CAL1NnmMxoHER2vdvhTsk4TR2zMtanHfURx=+J-PxqwjTB9p1dw@mail.gmail.com>
 <CA+X4w0wDjWx3idaNyLjjpCwrnj8K7OD1oOS4ZGQTUHK71mxxNg@mail.gmail.com>
 <CAL1NnmMjJEMFgy20TqRc35egF3-w4GPDjLnW-DW_as61jTG5Bw@mail.gmail.com>
 <CA+X4w0y921S3hRPQ7PMzTOBz-=Tw33xTojpQmqL0JkN6DnAj9g@mail.gmail.com>
 <CAL1NnmMDuSuqtx23HTUjep7FBewXUd=xf-z50i57GYyNgSL_BQ@mail.gmail.com>
 <CAL1NnmMk+3T-XMYr9eoT6j5fu83GGkY7cyS0Et4pzGRbjFJU9w@mail.gmail.com>
 <CA+X4w0yD6QMOc=h4qNnRVcwkwaT7rZHvMT2KdJDjU3xhBT8pMg@mail.gmail.com>
Message-ID: <CAL1NnmOoR-wgzcNiQ-Vjb1zCPRfLWh_8n0q9EREYwqSt2rbx_w@mail.gmail.com>

HI Ariel,
Thank you so much for the code and it ran without any errors.
However, i am still puzzled what my scripts failed, which i do not see the
differences between yours and mine.

Regards,

Ping

On Thu, Jan 10, 2019 at 6:27 PM Ariel Rokem <arokem at gmail.com> wrote:

> Hi Ping,
>
> Sorry. Using your mask, I can't reproduce the error. Here is my code:
> https://gist.github.com/arokem/2b7963ad5bd625f24e60c4a9307e7b7c
>
> I'd make sure to get rid of all the nans first (although I didn't seem to
> need to do this in my implementation).
>
> Hope that helps,
>
> Ariel
>
> On Wed, Jan 9, 2019 at 4:47 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
> wrote:
>
>> Hi Ariel
>>
>> Have you got the mask file?
>>
>> Any update?
>>
>> Thanks!
>> Ping
>>
>> On Fri, Jan 4, 2019 at 1:31 PM Ping-Hong Yeh <pinghongyeh at gmail.com>
>> wrote:
>>
>>> I have attached the mask file.  Thank you.
>>>
>>> maskimg = nib.load(join(dname, 'structural_mask.nii.gz'))
>>> mask = maskimg.get_data()
>>> affinemask = maskimg.affine
>>>
>>>
>>> On Fri, Jan 4, 2019 at 1:13 PM Ariel Rokem <arokem at gmail.com> wrote:
>>>
>>>>
>>>> On Fri, Jan 4, 2019 at 7:42 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi Ariel,
>>>>>
>>>>> Thank you for your time.
>>>>>  I've run fslmaths using the syntax of -nan  beforehand, i thought
>>>>> that has taken care of it.
>>>>>
>>>>
>>>> I believe it's still there. My script crashed on that.
>>>>
>>>>
>>>>> Here is the script i used,
>>>>>
>>>>> import dipy.reconst.fwdti as fwdti
>>>>> Delta = 22.536
>>>>> delta = 21.908
>>>>> _Delta = 0.022536
>>>>> _delta = 0.021908
>>>>>
>>>>> dname=os.path.join('/data/NEURO2/ping/MUX', id,
>>>>> 'SOA_N270_plus19b0_fwd','data_DIFFPREP_t2acpc_proc_DRBUDDI_proc')
>>>>> fdwi = join(dname,
>>>>> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0_nan.nii.gz')
>>>>> fbvec = join(dname,
>>>>> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0_invY.bvecs') #the final
>>>>> oriention after TORTOISE is RAS for earlier SOA289 data
>>>>> fbval = join(dname,
>>>>> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0.bvals')
>>>>>
>>>>> from dipy.io import read_bvals_bvecs
>>>>> bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
>>>>> from dipy.core.gradients import gradient_table
>>>>> gtab = gradient_table(bvals, bvecs, big_delta=Delta, small_delta=delta)
>>>>> img = nib.load(fdwi)
>>>>> data = img.get_data()
>>>>> affine = img.affine
>>>>>
>>>>> #free water
>>>>> fwdtimodel = fwdti.FreeWaterTensorModel(gtab, fit_method='NLS' )
>>>>> fwdtifit = fwdtimodel.fit(data, mask=mask)
>>>>> img = nib.Nifti1Image(fwdtifit.fa, affine)
>>>>> nib.save(img, join(dname, 'FWdti_FA.nii.gz'))
>>>>> img = nib.Nifti1Image(fwdtifit.md, affine)
>>>>> nib.save(img, join(dname, 'FWdti_MD.nii.gz'))
>>>>> img = nib.Nifti1Image(fwdtifit.ad, affine)
>>>>> nib.save(img, join(dname, 'FWdti_AD.nii.gz'))
>>>>> img = nib.Nifti1Image(fwdtifit.rd, affine)
>>>>> nib.save(img, join(dname, 'FWdti_RD.nii.gz'))
>>>>> img = nib.Nifti1Image(fwdtifit.f, affine)
>>>>> nib.save(img, join(dname, 'FWdti_fw.nii.gz'))
>>>>>
>>>>>
>>>> Where did `mask` come from?
>>>>
>>>> Cheers,
>>>>
>>>> Ariel
>>>>
>>>>>
>>>>> On Fri, Jan 4, 2019 at 9:23 AM Ariel Rokem <arokem at gmail.com> wrote:
>>>>>
>>>>>> Hi Ping,
>>>>>>
>>>>>> I can't quite reproduce your error, though I am getting similar
>>>>>> errors. Could you also share the code that you are running?
>>>>>>
>>>>>> For the time being, the one thing that I noticed is that there are
>>>>>> NaNs in your data. That might be causing this issue.
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> Ariel
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Mon, Dec 31, 2018 at 5:43 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Ariel,
>>>>>>>
>>>>>>>  Have you got the chance to look at the DWI data that was attached
>>>>>>> to the previous email?
>>>>>>>
>>>>>>> Thank you for your time.
>>>>>>>
>>>>>>> Ping
>>>>>>>
>>>>>>> On Sat, Dec 29, 2018 at 1:12 AM Ariel Rokem <arokem at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi Ping,
>>>>>>>>
>>>>>>>> Thanks for your email. Hard to say exactly what is going on without
>>>>>>>> further information. Could you tell us more about the data you are using?
>>>>>>>> How many b-values? How many directions? Any chance you could share the data
>>>>>>>> from the voxel that caused that error to be raised?
>>>>>>>>
>>>>>>>> Thanks!
>>>>>>>>
>>>>>>>> Ariel
>>>>>>>>
>>>>>>>> On Thu, Dec 27, 2018 at 6:55 AM Ping-Hong Yeh <
>>>>>>>> pinghongyeh at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Hi Dipy Users,
>>>>>>>>>
>>>>>>>>>  I've ran into errors "Eigenvalues did not  converge" when using
>>>>>>>>> the free water elimination model,
>>>>>>>>> and here is the error message:
>>>>>>>>>
>>>>>>>>>   File
>>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>>>>>>>> line 1615, in _decompose_tensor_nan
>>>>>>>>>     min_diffusivity=min_diffusivity)
>>>>>>>>>   File
>>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>>>>>>>> line 1946, in decompose_tensor
>>>>>>>>>     eigenvals, eigenvecs = eigh(tensor)
>>>>>>>>>   File
>>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/utils/arrfuncs.py",
>>>>>>>>> line 128, in eigh
>>>>>>>>>     return np.linalg.eigh(a, UPLO)
>>>>>>>>>   File
>>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>>>>>>>> line 1291, in eigh
>>>>>>>>>     w, vt = gufunc(a, signature=signature, extobj=extobj)
>>>>>>>>>   File
>>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>>>>>>>> line 95, in _raise_linalgerror_eigenvalues_nonconvergence
>>>>>>>>>     raise LinAlgError("Eigenvalues did not converge")
>>>>>>>>> numpy.linalg.linalg.LinAlgError: Eigenvalues did not converge
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Any suggestions?
>>>>>>>>>
>>>>>>>>> Thank you.
>>>>>>>>>
>>>>>>>>> Ping
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Neuroimaging mailing list
>>>>>>>>> Neuroimaging at python.org
>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Neuroimaging mailing list
>>>>>>>> Neuroimaging at python.org
>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Neuroimaging mailing list
>>>>>>> Neuroimaging at python.org
>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>
>>>>>> _______________________________________________
>>>>>> Neuroimaging mailing list
>>>>>> Neuroimaging at python.org
>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>
>>>>> _______________________________________________
>>>>> Neuroimaging mailing list
>>>>> Neuroimaging at python.org
>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>
>>>> _______________________________________________
>>>> Neuroimaging mailing list
>>>> Neuroimaging at python.org
>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>
>>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From elef at indiana.edu  Sat Jan 12 17:55:01 2019
From: elef at indiana.edu (Eleftherios Garyfallidis)
Date: Sat, 12 Jan 2019 17:55:01 -0500
Subject: [Neuroimaging] failure using DIPY Free Water Elimination DTI
In-Reply-To: <CAL1NnmOoR-wgzcNiQ-Vjb1zCPRfLWh_8n0q9EREYwqSt2rbx_w@mail.gmail.com>
References: <CAL1NnmNTd0z+k7-bu1+PSAk_zdcEdK2Yk+jPKAWzC0wt2CUCZA@mail.gmail.com>
 <CA+X4w0zE_wDfF3xFMBcT2ryhherw+esHOS4guhk98q614yT4AA@mail.gmail.com>
 <CAL1NnmMxoHER2vdvhTsk4TR2zMtanHfURx=+J-PxqwjTB9p1dw@mail.gmail.com>
 <CA+X4w0wDjWx3idaNyLjjpCwrnj8K7OD1oOS4ZGQTUHK71mxxNg@mail.gmail.com>
 <CAL1NnmMjJEMFgy20TqRc35egF3-w4GPDjLnW-DW_as61jTG5Bw@mail.gmail.com>
 <CA+X4w0y921S3hRPQ7PMzTOBz-=Tw33xTojpQmqL0JkN6DnAj9g@mail.gmail.com>
 <CAL1NnmMDuSuqtx23HTUjep7FBewXUd=xf-z50i57GYyNgSL_BQ@mail.gmail.com>
 <CAL1NnmMk+3T-XMYr9eoT6j5fu83GGkY7cyS0Et4pzGRbjFJU9w@mail.gmail.com>
 <CA+X4w0yD6QMOc=h4qNnRVcwkwaT7rZHvMT2KdJDjU3xhBT8pMg@mail.gmail.com>
 <CAL1NnmOoR-wgzcNiQ-Vjb1zCPRfLWh_8n0q9EREYwqSt2rbx_w@mail.gmail.com>
Message-ID: <CAN6JmWM1j8DsDENxOsSNZ-mUn-wPAeN5Y3pHwVqp9MP3CvgvsA@mail.gmail.com>

Must be magic :)

On Sat, Jan 12, 2019 at 4:17 PM Ping-Hong Yeh <pinghongyeh at gmail.com> wrote:

> HI Ariel,
> Thank you so much for the code and it ran without any errors.
> However, i am still puzzled what my scripts failed, which i do not see the
> differences between yours and mine.
>
> Regards,
>
> Ping
>
> On Thu, Jan 10, 2019 at 6:27 PM Ariel Rokem <arokem at gmail.com> wrote:
>
>> Hi Ping,
>>
>> Sorry. Using your mask, I can't reproduce the error. Here is my code:
>> https://gist.github.com/arokem/2b7963ad5bd625f24e60c4a9307e7b7c
>>
>> I'd make sure to get rid of all the nans first (although I didn't seem to
>> need to do this in my implementation).
>>
>> Hope that helps,
>>
>> Ariel
>>
>> On Wed, Jan 9, 2019 at 4:47 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>> wrote:
>>
>>> Hi Ariel
>>>
>>> Have you got the mask file?
>>>
>>> Any update?
>>>
>>> Thanks!
>>> Ping
>>>
>>> On Fri, Jan 4, 2019 at 1:31 PM Ping-Hong Yeh <pinghongyeh at gmail.com>
>>> wrote:
>>>
>>>> I have attached the mask file.  Thank you.
>>>>
>>>> maskimg = nib.load(join(dname, 'structural_mask.nii.gz'))
>>>> mask = maskimg.get_data()
>>>> affinemask = maskimg.affine
>>>>
>>>>
>>>> On Fri, Jan 4, 2019 at 1:13 PM Ariel Rokem <arokem at gmail.com> wrote:
>>>>
>>>>>
>>>>> On Fri, Jan 4, 2019 at 7:42 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi Ariel,
>>>>>>
>>>>>> Thank you for your time.
>>>>>>  I've run fslmaths using the syntax of -nan  beforehand, i thought
>>>>>> that has taken care of it.
>>>>>>
>>>>>
>>>>> I believe it's still there. My script crashed on that.
>>>>>
>>>>>
>>>>>> Here is the script i used,
>>>>>>
>>>>>> import dipy.reconst.fwdti as fwdti
>>>>>> Delta = 22.536
>>>>>> delta = 21.908
>>>>>> _Delta = 0.022536
>>>>>> _delta = 0.021908
>>>>>>
>>>>>> dname=os.path.join('/data/NEURO2/ping/MUX', id,
>>>>>> 'SOA_N270_plus19b0_fwd','data_DIFFPREP_t2acpc_proc_DRBUDDI_proc')
>>>>>> fdwi = join(dname,
>>>>>> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0_nan.nii.gz')
>>>>>> fbvec = join(dname,
>>>>>> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0_invY.bvecs') #the final
>>>>>> oriention after TORTOISE is RAS for earlier SOA289 data
>>>>>> fbval = join(dname,
>>>>>> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0.bvals')
>>>>>>
>>>>>> from dipy.io import read_bvals_bvecs
>>>>>> bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
>>>>>> from dipy.core.gradients import gradient_table
>>>>>> gtab = gradient_table(bvals, bvecs, big_delta=Delta,
>>>>>> small_delta=delta)
>>>>>> img = nib.load(fdwi)
>>>>>> data = img.get_data()
>>>>>> affine = img.affine
>>>>>>
>>>>>> #free water
>>>>>> fwdtimodel = fwdti.FreeWaterTensorModel(gtab, fit_method='NLS' )
>>>>>> fwdtifit = fwdtimodel.fit(data, mask=mask)
>>>>>> img = nib.Nifti1Image(fwdtifit.fa, affine)
>>>>>> nib.save(img, join(dname, 'FWdti_FA.nii.gz'))
>>>>>> img = nib.Nifti1Image(fwdtifit.md, affine)
>>>>>> nib.save(img, join(dname, 'FWdti_MD.nii.gz'))
>>>>>> img = nib.Nifti1Image(fwdtifit.ad, affine)
>>>>>> nib.save(img, join(dname, 'FWdti_AD.nii.gz'))
>>>>>> img = nib.Nifti1Image(fwdtifit.rd, affine)
>>>>>> nib.save(img, join(dname, 'FWdti_RD.nii.gz'))
>>>>>> img = nib.Nifti1Image(fwdtifit.f, affine)
>>>>>> nib.save(img, join(dname, 'FWdti_fw.nii.gz'))
>>>>>>
>>>>>>
>>>>> Where did `mask` come from?
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Ariel
>>>>>
>>>>>>
>>>>>> On Fri, Jan 4, 2019 at 9:23 AM Ariel Rokem <arokem at gmail.com> wrote:
>>>>>>
>>>>>>> Hi Ping,
>>>>>>>
>>>>>>> I can't quite reproduce your error, though I am getting similar
>>>>>>> errors. Could you also share the code that you are running?
>>>>>>>
>>>>>>> For the time being, the one thing that I noticed is that there are
>>>>>>> NaNs in your data. That might be causing this issue.
>>>>>>>
>>>>>>> Cheers,
>>>>>>>
>>>>>>> Ariel
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Dec 31, 2018 at 5:43 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi Ariel,
>>>>>>>>
>>>>>>>>  Have you got the chance to look at the DWI data that was attached
>>>>>>>> to the previous email?
>>>>>>>>
>>>>>>>> Thank you for your time.
>>>>>>>>
>>>>>>>> Ping
>>>>>>>>
>>>>>>>> On Sat, Dec 29, 2018 at 1:12 AM Ariel Rokem <arokem at gmail.com>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Hi Ping,
>>>>>>>>>
>>>>>>>>> Thanks for your email. Hard to say exactly what is going on
>>>>>>>>> without further information. Could you tell us more about the data you are
>>>>>>>>> using? How many b-values? How many directions? Any chance you could share
>>>>>>>>> the data from the voxel that caused that error to be raised?
>>>>>>>>>
>>>>>>>>> Thanks!
>>>>>>>>>
>>>>>>>>> Ariel
>>>>>>>>>
>>>>>>>>> On Thu, Dec 27, 2018 at 6:55 AM Ping-Hong Yeh <
>>>>>>>>> pinghongyeh at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Dipy Users,
>>>>>>>>>>
>>>>>>>>>>  I've ran into errors "Eigenvalues did not  converge" when using
>>>>>>>>>> the free water elimination model,
>>>>>>>>>> and here is the error message:
>>>>>>>>>>
>>>>>>>>>>   File
>>>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>>>>>>>>> line 1615, in _decompose_tensor_nan
>>>>>>>>>>     min_diffusivity=min_diffusivity)
>>>>>>>>>>   File
>>>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>>>>>>>>> line 1946, in decompose_tensor
>>>>>>>>>>     eigenvals, eigenvecs = eigh(tensor)
>>>>>>>>>>   File
>>>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/utils/arrfuncs.py",
>>>>>>>>>> line 128, in eigh
>>>>>>>>>>     return np.linalg.eigh(a, UPLO)
>>>>>>>>>>   File
>>>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>>>>>>>>> line 1291, in eigh
>>>>>>>>>>     w, vt = gufunc(a, signature=signature, extobj=extobj)
>>>>>>>>>>   File
>>>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>>>>>>>>> line 95, in _raise_linalgerror_eigenvalues_nonconvergence
>>>>>>>>>>     raise LinAlgError("Eigenvalues did not converge")
>>>>>>>>>> numpy.linalg.linalg.LinAlgError: Eigenvalues did not converge
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Any suggestions?
>>>>>>>>>>
>>>>>>>>>> Thank you.
>>>>>>>>>>
>>>>>>>>>> Ping
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Neuroimaging mailing list
>>>>>>>>> Neuroimaging at python.org
>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Neuroimaging mailing list
>>>>>>>> Neuroimaging at python.org
>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Neuroimaging mailing list
>>>>>>> Neuroimaging at python.org
>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>
>>>>>> _______________________________________________
>>>>>> Neuroimaging mailing list
>>>>>> Neuroimaging at python.org
>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>
>>>>> _______________________________________________
>>>>> Neuroimaging mailing list
>>>>> Neuroimaging at python.org
>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>
>>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From arokem at gmail.com  Mon Jan 14 00:20:04 2019
From: arokem at gmail.com (Ariel Rokem)
Date: Sun, 13 Jan 2019 21:20:04 -0800
Subject: [Neuroimaging] failure using DIPY Free Water Elimination DTI
In-Reply-To: <CAN6JmWM1j8DsDENxOsSNZ-mUn-wPAeN5Y3pHwVqp9MP3CvgvsA@mail.gmail.com>
References: <CAL1NnmNTd0z+k7-bu1+PSAk_zdcEdK2Yk+jPKAWzC0wt2CUCZA@mail.gmail.com>
 <CA+X4w0zE_wDfF3xFMBcT2ryhherw+esHOS4guhk98q614yT4AA@mail.gmail.com>
 <CAL1NnmMxoHER2vdvhTsk4TR2zMtanHfURx=+J-PxqwjTB9p1dw@mail.gmail.com>
 <CA+X4w0wDjWx3idaNyLjjpCwrnj8K7OD1oOS4ZGQTUHK71mxxNg@mail.gmail.com>
 <CAL1NnmMjJEMFgy20TqRc35egF3-w4GPDjLnW-DW_as61jTG5Bw@mail.gmail.com>
 <CA+X4w0y921S3hRPQ7PMzTOBz-=Tw33xTojpQmqL0JkN6DnAj9g@mail.gmail.com>
 <CAL1NnmMDuSuqtx23HTUjep7FBewXUd=xf-z50i57GYyNgSL_BQ@mail.gmail.com>
 <CAL1NnmMk+3T-XMYr9eoT6j5fu83GGkY7cyS0Et4pzGRbjFJU9w@mail.gmail.com>
 <CA+X4w0yD6QMOc=h4qNnRVcwkwaT7rZHvMT2KdJDjU3xhBT8pMg@mail.gmail.com>
 <CAL1NnmOoR-wgzcNiQ-Vjb1zCPRfLWh_8n0q9EREYwqSt2rbx_w@mail.gmail.com>
 <CAN6JmWM1j8DsDENxOsSNZ-mUn-wPAeN5Y3pHwVqp9MP3CvgvsA@mail.gmail.com>
Message-ID: <CA+X4w0zDkeJ_JE1n6K6YEFS1pgPX=SKc=AH3VfmGXXnyKaR5SA@mail.gmail.com>

On Sat, Jan 12, 2019 at 2:56 PM Eleftherios Garyfallidis <elef at indiana.edu>
wrote:

> Must be magic :)
>
> On Sat, Jan 12, 2019 at 4:17 PM Ping-Hong Yeh <pinghongyeh at gmail.com>
> wrote:
>
>> HI Ariel,
>> Thank you so much for the code and it ran without any errors.
>> However, i am still puzzled what my scripts failed, which i do not see
>> the differences between yours and mine.
>>
>> Yeah - I have no idea. But happy to hear that it works for you :-)

Ariel


> Regards,
>>
>> Ping
>>
>> On Thu, Jan 10, 2019 at 6:27 PM Ariel Rokem <arokem at gmail.com> wrote:
>>
>>> Hi Ping,
>>>
>>> Sorry. Using your mask, I can't reproduce the error. Here is my code:
>>> https://gist.github.com/arokem/2b7963ad5bd625f24e60c4a9307e7b7c
>>>
>>> I'd make sure to get rid of all the nans first (although I didn't seem
>>> to need to do this in my implementation).
>>>
>>> Hope that helps,
>>>
>>> Ariel
>>>
>>> On Wed, Jan 9, 2019 at 4:47 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>>> wrote:
>>>
>>>> Hi Ariel
>>>>
>>>> Have you got the mask file?
>>>>
>>>> Any update?
>>>>
>>>> Thanks!
>>>> Ping
>>>>
>>>> On Fri, Jan 4, 2019 at 1:31 PM Ping-Hong Yeh <pinghongyeh at gmail.com>
>>>> wrote:
>>>>
>>>>> I have attached the mask file.  Thank you.
>>>>>
>>>>> maskimg = nib.load(join(dname, 'structural_mask.nii.gz'))
>>>>> mask = maskimg.get_data()
>>>>> affinemask = maskimg.affine
>>>>>
>>>>>
>>>>> On Fri, Jan 4, 2019 at 1:13 PM Ariel Rokem <arokem at gmail.com> wrote:
>>>>>
>>>>>>
>>>>>> On Fri, Jan 4, 2019 at 7:42 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Ariel,
>>>>>>>
>>>>>>> Thank you for your time.
>>>>>>>  I've run fslmaths using the syntax of -nan  beforehand, i thought
>>>>>>> that has taken care of it.
>>>>>>>
>>>>>>
>>>>>> I believe it's still there. My script crashed on that.
>>>>>>
>>>>>>
>>>>>>> Here is the script i used,
>>>>>>>
>>>>>>> import dipy.reconst.fwdti as fwdti
>>>>>>> Delta = 22.536
>>>>>>> delta = 21.908
>>>>>>> _Delta = 0.022536
>>>>>>> _delta = 0.021908
>>>>>>>
>>>>>>> dname=os.path.join('/data/NEURO2/ping/MUX', id,
>>>>>>> 'SOA_N270_plus19b0_fwd','data_DIFFPREP_t2acpc_proc_DRBUDDI_proc')
>>>>>>> fdwi = join(dname,
>>>>>>> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0_nan.nii.gz')
>>>>>>> fbvec = join(dname,
>>>>>>> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0_invY.bvecs') #the final
>>>>>>> oriention after TORTOISE is RAS for earlier SOA289 data
>>>>>>> fbval = join(dname,
>>>>>>> 'data_DIFFPREP_t2acpc_proc_DRBUDDI_up_final_no7b0.bvals')
>>>>>>>
>>>>>>> from dipy.io import read_bvals_bvecs
>>>>>>> bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
>>>>>>> from dipy.core.gradients import gradient_table
>>>>>>> gtab = gradient_table(bvals, bvecs, big_delta=Delta,
>>>>>>> small_delta=delta)
>>>>>>> img = nib.load(fdwi)
>>>>>>> data = img.get_data()
>>>>>>> affine = img.affine
>>>>>>>
>>>>>>> #free water
>>>>>>> fwdtimodel = fwdti.FreeWaterTensorModel(gtab, fit_method='NLS' )
>>>>>>> fwdtifit = fwdtimodel.fit(data, mask=mask)
>>>>>>> img = nib.Nifti1Image(fwdtifit.fa, affine)
>>>>>>> nib.save(img, join(dname, 'FWdti_FA.nii.gz'))
>>>>>>> img = nib.Nifti1Image(fwdtifit.md, affine)
>>>>>>> nib.save(img, join(dname, 'FWdti_MD.nii.gz'))
>>>>>>> img = nib.Nifti1Image(fwdtifit.ad, affine)
>>>>>>> nib.save(img, join(dname, 'FWdti_AD.nii.gz'))
>>>>>>> img = nib.Nifti1Image(fwdtifit.rd, affine)
>>>>>>> nib.save(img, join(dname, 'FWdti_RD.nii.gz'))
>>>>>>> img = nib.Nifti1Image(fwdtifit.f, affine)
>>>>>>> nib.save(img, join(dname, 'FWdti_fw.nii.gz'))
>>>>>>>
>>>>>>>
>>>>>> Where did `mask` come from?
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> Ariel
>>>>>>
>>>>>>>
>>>>>>> On Fri, Jan 4, 2019 at 9:23 AM Ariel Rokem <arokem at gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi Ping,
>>>>>>>>
>>>>>>>> I can't quite reproduce your error, though I am getting similar
>>>>>>>> errors. Could you also share the code that you are running?
>>>>>>>>
>>>>>>>> For the time being, the one thing that I noticed is that there are
>>>>>>>> NaNs in your data. That might be causing this issue.
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>>
>>>>>>>> Ariel
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mon, Dec 31, 2018 at 5:43 AM Ping-Hong Yeh <
>>>>>>>> pinghongyeh at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Hi Ariel,
>>>>>>>>>
>>>>>>>>>  Have you got the chance to look at the DWI data that was attached
>>>>>>>>> to the previous email?
>>>>>>>>>
>>>>>>>>> Thank you for your time.
>>>>>>>>>
>>>>>>>>> Ping
>>>>>>>>>
>>>>>>>>> On Sat, Dec 29, 2018 at 1:12 AM Ariel Rokem <arokem at gmail.com>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Ping,
>>>>>>>>>>
>>>>>>>>>> Thanks for your email. Hard to say exactly what is going on
>>>>>>>>>> without further information. Could you tell us more about the data you are
>>>>>>>>>> using? How many b-values? How many directions? Any chance you could share
>>>>>>>>>> the data from the voxel that caused that error to be raised?
>>>>>>>>>>
>>>>>>>>>> Thanks!
>>>>>>>>>>
>>>>>>>>>> Ariel
>>>>>>>>>>
>>>>>>>>>> On Thu, Dec 27, 2018 at 6:55 AM Ping-Hong Yeh <
>>>>>>>>>> pinghongyeh at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Dipy Users,
>>>>>>>>>>>
>>>>>>>>>>>  I've ran into errors "Eigenvalues did not  converge" when using
>>>>>>>>>>> the free water elimination model,
>>>>>>>>>>> and here is the error message:
>>>>>>>>>>>
>>>>>>>>>>>   File
>>>>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>>>>>>>>>> line 1615, in _decompose_tensor_nan
>>>>>>>>>>>     min_diffusivity=min_diffusivity)
>>>>>>>>>>>   File
>>>>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>>>>>>>>>> line 1946, in decompose_tensor
>>>>>>>>>>>     eigenvals, eigenvecs = eigh(tensor)
>>>>>>>>>>>   File
>>>>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/utils/arrfuncs.py",
>>>>>>>>>>> line 128, in eigh
>>>>>>>>>>>     return np.linalg.eigh(a, UPLO)
>>>>>>>>>>>   File
>>>>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>>>>>>>>>> line 1291, in eigh
>>>>>>>>>>>     w, vt = gufunc(a, signature=signature, extobj=extobj)
>>>>>>>>>>>   File
>>>>>>>>>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>>>>>>>>>> line 95, in _raise_linalgerror_eigenvalues_nonconvergence
>>>>>>>>>>>     raise LinAlgError("Eigenvalues did not converge")
>>>>>>>>>>> numpy.linalg.linalg.LinAlgError: Eigenvalues did not converge
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Any suggestions?
>>>>>>>>>>>
>>>>>>>>>>> Thank you.
>>>>>>>>>>>
>>>>>>>>>>> Ping
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Neuroimaging mailing list
>>>>>>>>> Neuroimaging at python.org
>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Neuroimaging mailing list
>>>>>>>> Neuroimaging at python.org
>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Neuroimaging mailing list
>>>>>>> Neuroimaging at python.org
>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>
>>>>>> _______________________________________________
>>>>>> Neuroimaging mailing list
>>>>>> Neuroimaging at python.org
>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>
>>>>> _______________________________________________
>>>> Neuroimaging mailing list
>>>> Neuroimaging at python.org
>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From newsletter at a2mailserver.com  Wed Jan  9 22:50:09 2019
From: newsletter at a2mailserver.com (Avraham F)
Date: Thu, 10 Jan 2019 04:50:09 +0100
Subject: [Neuroimaging] Call for abstract (2019) Tel Aviv
Message-ID: <0.0.1.97.1D4A89795492964.0@erricson.jartent.info>

Your email client cannot read this email. To view it online, please go here: http://track.yoganews.info/campaigns/webversion/NzcwNg==/MzI3OTQwNg==/MjU5<br />If you received this email by mistake - we apologize and please?Unsubscribe me from this list<br /><br />?<br /><br />Dear colleagues,<br /><br />?<br /><br />You are welcome to join us in the 2019 International Conference on?"Movement and Cognition" which will take place on 22-24 July 2019? at the Tel-Aviv University, Israel.<br /><br />The event addresses the relationship between movement and cognition and the broad topic of the conference include?scientific explorations?of Cognitive-Movement applications.<br /><br />?<br /><br />You are welcome also to submit to the scientific committee an abstract for oral presentation, poster, symposium, or workshop,? if you wish to present your work or research at the conference.<br /><br /><br /><br /><br />For more details please check out our conference website at: www.movementis.co.il<br /><br />?<br /><br />Should you have questions relating to the conference, please contact the conference organizers at:?office at movememntis.com ?<br /><br />?<br /><br />I hope to meet you in Tel-Aviv in July 2019.<br /><br />Wish very best wishes,<br /><br />?<br /><br />Gerry Leisman<br /><br />Full Professor Neuro-?&?Rehabilitation Sciences and Research Fellow<br /><br />University of Haifa<br /><br />Faculty of Social Welfare and Health Sciences<br /><br />Abba Khoushy Ave. 199,?Eshkol Tower, Rm. 910<br /><br />Mt. Carmel, Haifa, Israel 3498838<br /><br />Profesor de Neurolog?a Restaurativa<br /><br />Universidad de Ciencias M?dicas<br /><br />Facultad 'Manuel Fajardo'<br /><br />Instituto de Neurolog?a y Neurocirug?a<br /><br />Neurofisiolog?a Clin?ca<br /><br />Ciudad de la Habana, Cuba?<br /><br />+(972)-(0)52-420-5643 [Israel] ; ?<br /><br />+1-516-301-5305?[Office/Labs Both USA and?Israel] University Email:?g.leisman at edu.haifa.ac.il<br /><br />?<br /><br />
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From gbcosme at fc.ul.pt  Mon Jan 14 12:11:48 2019
From: gbcosme at fc.ul.pt (gcosme)
Date: Mon, 14 Jan 2019 17:11:48 +0000
Subject: [Neuroimaging] Two Post-Doc positions opened at the Biomedical
 Neuroscience Lab in Lisbon
Message-ID: <00d2a734ec1e4ae5b466b5a12f87a608@FC-MBX1.fc.ul.pt>

?

Two Post-Doc positions opened at the Biomedical Neuroscience Lab (https://dpratalab.wordpress.com/; PI: Dr Diana Prata, with double affiliation in King's College London), at the University of Lisbon - for research in human social neuroscience and the oxytocin and the dopamine systems in a highly interdisciplinary 3-year project involving pharmacology, genetics and a range of psychophysiological techniques. Expertise in fMRI and/or EEG highly preferred; and in eye-tracking and SCR favourable. Negotiable salary. Open until 26th of Jan 2019. We look forward to welcoming you!

http://www.eracareers.pt/opportunities/index.aspx?task=global&jobId=106526?


Best,

Cosmo

Gon?alo Bairos Cosme
________________________________
Biomedical Neuroscience Lab - Diana Prata's Lab
Instituto de Biof?sica e Engenharia Biom?dica
Faculdade de Ci?ncias da Universidade de Lisboa
Campo Grande - 1749-016 Lisboa


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From markiewicz at stanford.edu  Wed Jan 16 10:17:17 2019
From: markiewicz at stanford.edu (Christopher Markiewicz)
Date: Wed, 16 Jan 2019 15:17:17 +0000
Subject: [Neuroimaging] ANN: nibabel 2.3.3
Message-ID: <BN6PR02MB2675085710DC9F0512C4333FA9820@BN6PR02MB2675.namprd02.prod.outlook.com>

Hi all,


Some of you may have noticed import issues with the nibabel 2.3.2 release. Due to some changes in the build scripts, the six library was no longer being required.


The latest 2.3.3 release is simply 2.3.2 with fixed dependencies, so there's no urgent need to upgrade if your installation is working fine. Any libraries would probably do well to avoid pinning to 2.3.2, however.


Thanks to Gael Varoquaux and the rest of the nilearn team for tracking down the issue.


Please cite the latest nibabel using the Zenodo DOI: https://doi.org/10.5281/zenodo.2541736


--

Chris Markiewicz

Center for Reproducible Neuroscience

Stanford University
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From baran.aydogan at aalto.fi  Wed Jan 16 13:06:41 2019
From: baran.aydogan at aalto.fi (Aydogan Baran)
Date: Wed, 16 Jan 2019 18:06:41 +0000
Subject: [Neuroimaging] Brain Twitter Conference 2019 #brainTC
Message-ID: <895752e970f54c1ba4f24f9e7fa7815d@aalto.fi>

Dear colleagues,

The 3rd Annual Brain Twitter Conference 2019 (#brainTC) will take place on March 14th, 2019 and the abstract submission is now open!

This year the keynote tweeters include Russ Poldrack (@russpoldrack?) and Jay van Bavel (@jayvanbavel)! For more information about the conference and how to submit an abstract, please visit our website https://brain.tc and follow @RealBrainTC.

We would also appreciate if can spread the call in your networks!

What is Twitter Conference?

A Twitter conference is meant for scientists to present and discuss their research on social media. During the conference presenters will be allocated a 15 min time slot, during which they will present a series of 6 tweets or less, marked with the #brainTC tag and an ordinal number of the tweet. This is a great opportunity to practice condensing your message and getting word of your research out there. In the last two years #brainTC has a reached an average of ~ 0.5 million Twitter users!

On behalf of the organizing committee, best wishes,

D. Baran Aydogan
@baranaydogan

--
D. Baran Aydogan, PhD

Post Doctoral Researcher
Department of Neuroscience and Biomedical Engineering
Aalto University, Finland
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From gael.varoquaux at normalesup.org  Thu Jan 17 09:31:01 2019
From: gael.varoquaux at normalesup.org (Gael Varoquaux)
Date: Thu, 17 Jan 2019 15:31:01 +0100
Subject: [Neuroimaging] ANN: nibabel 2.3.3
In-Reply-To: <BN6PR02MB2675085710DC9F0512C4333FA9820@BN6PR02MB2675.namprd02.prod.outlook.com>
References: <BN6PR02MB2675085710DC9F0512C4333FA9820@BN6PR02MB2675.namprd02.prod.outlook.com>
Message-ID: <20190117143101.e74ura3nlwervwfg@phare.normalesup.org>

On Wed, Jan 16, 2019 at 03:17:17PM +0000, Christopher Markiewicz wrote:
> Thanks to Gael Varoquaux and the rest of the nilearn team for tracking down the
> issue.

Thanks to you and the rest of the team for being incredibly responsive.
You are doing a service to the community.

Ga?l

From j.schreiber at fz-juelich.de  Fri Jan 18 04:14:22 2019
From: j.schreiber at fz-juelich.de (Jan Schreiber)
Date: Fri, 18 Jan 2019 10:14:22 +0100
Subject: [Neuroimaging] [DIPY] Calculate Path Length Map
Message-ID: <4c59cc61-3eb9-42fb-7f1c-c970300c4010@fz-juelich.de>

Dear Experts,

I am trying to run the "Calculate Path Length Map" example
http://nipy.org/dipy/examples_built/path_length_map.html#example-path-length-map

Unfortunately I am getting the error message

Traceback (most recent call last):
   File "path_length_map.py", line 26, in <module>
     from dipy.viz import actor, window, colormap as cmap
ImportError: cannot import name 'actor'


Python 3.6.7 :: Anaconda custom (64-bit)
dipy==0.15.0
vtk==8.1.2

Do you have an idea what's missing?

Thanks,
Jan

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From skoudoro at iu.edu  Fri Jan 18 09:27:43 2019
From: skoudoro at iu.edu (Koudoro, Serge)
Date: Fri, 18 Jan 2019 14:27:43 +0000
Subject: [Neuroimaging] [DIPY] Calculate Path Length Map
In-Reply-To: <4c59cc61-3eb9-42fb-7f1c-c970300c4010@fz-juelich.de>
References: <4c59cc61-3eb9-42fb-7f1c-c970300c4010@fz-juelich.de>
Message-ID: <d10828292d4f49108680e9e1829fbc73@BL-CCI-D1S06.ads.iu.edu>

Hi Jan,

Try to install FURY package (https://github.com/fury-gl/fury):

-> pip install fury

It should work after that. 

Serge K.

--- DIPY Workshop 2019, Titanium Edition --- March 11-15 --- More information at https://workshop.dipy.org


-----Original Message-----
From: Neuroimaging <neuroimaging-bounces+skoudoro=iu.edu at python.org> On Behalf Of Jan Schreiber
Sent: Friday, January 18, 2019 4:14 AM
To: Neuroimaging analysis in Python <neuroimaging at python.org>
Subject: [Neuroimaging] [DIPY] Calculate Path Length Map

Dear Experts,

I am trying to run the "Calculate Path Length Map" example http://nipy.org/dipy/examples_built/path_length_map.html#example-path-length-map

Unfortunately I am getting the error message

Traceback (most recent call last):
   File "path_length_map.py", line 26, in <module>
     from dipy.viz import actor, window, colormap as cmap
ImportError: cannot import name 'actor'


Python 3.6.7 :: Anaconda custom (64-bit)
dipy==0.15.0
vtk==8.1.2

Do you have an idea what's missing?

Thanks,
Jan


From eric.condamine at univ-grenoble-alpes.fr  Fri Jan 18 11:42:16 2019
From: eric.condamine at univ-grenoble-alpes.fr (Eric Condamine)
Date: Fri, 18 Jan 2019 17:42:16 +0100
Subject: [Neuroimaging] Fwd: Re: Apply resolution of one image.nii to
 another image.nii
In-Reply-To: <676271529.16972194.1547222862788.JavaMail.zimbra@inria.fr>
References: <676271529.16972194.1547222862788.JavaMail.zimbra@inria.fr>
Message-ID: <4a30a721-5ac7-e981-befb-e22f65f83305@univ-grenoble-alpes.fr>

Hello nipy experts,

Many thanks to Bertrand Thirion and Matthew Brett for their fast and 
suitable answers ! i.e. nilearn.image.resample_to_img() and 
nibabel.processing.resample_from_to(), respectively.

I tested these 2 possibilities, in addition to my proposal (skimage) and 
using as a reference the results obtained from imcalc (SPM), for the 
comparison (I don't know it is the best reference ... but it is mine :-))

1- I definitely not recommend my proposal !!! It was the less good 
result obtained ....

2- all these methods (including imcalc) make the header of the resized 
image from the header of the reference (especially the affine 
parameter). So, to obtain a good result, it is better to use images in 
the same space and position (i.e. after coregistration and normalisation).

3- As warned by Matthew, it was sometimes necessary to threshold the 
resized image with the nibabel.processing.resample_from_to() option. 
Indeed, the background with zero intensity in the original image was no 
longer zero in the resized image. This was not observed in all tests and 
I didn't take the time to investigate why. This was never necessary with 
the nilearn.image.resample_to_img(), in the same tests.

4- Except this non-zero intensity in the background of the resized image 
with nibabel.processing.resample_from_to(), and only in some cases, I 
obtained with nibabel.processing.resample_from_to() and 
nilearn.image.resample_to_img(), results very, very close of what it was 
possible to obtain with imcalc of SPM.

Again, thank you very much for your help !

Eric

**************************

Script used:


## *imcalc*

matlabbatch{1}.spm.util.imcalc.input = {
'/home/econdami/Desktop/test_resizeSPM/test1/ref.nii,1'
'/home/econdami/Desktop/test_resizeSPM/test1/mask.nii,1'
 ??????????????????????????????????????? };
matlabbatch{1}.spm.util.imcalc.output = 'output_image';
matlabbatch{1}.spm.util.imcalc.outdir = 
{'/home/econdami/Desktop/test_resizeSPM/test1/'};
matlabbatch{1}.spm.util.imcalc.expression = 'i2';
matlabbatch{1}.spm.util.imcalc.options.dmtx = 0;
matlabbatch{1}.spm.util.imcalc.options.mask = 0;
matlabbatch{1}.spm.util.imcalc.options.interp = 1;
matlabbatch{1}.spm.util.imcalc.options.dtype = 4;


## *nilearn.image*

from nilearn.image import resample_to_img
import nibabel as nib

output=resample_to_img('/home/econdami/Desktop/test_resize/test_resizeNilearn/mask.nii', 
'/home/econdami/Desktop/test_resize/test_resizeNilearn/ref.nii')
nib.save(output, 
'/home/econdami/Desktop/test_resize/test_resizeNilearn/output_image')


## *nilearn.image*

import nibabel.processing as nibp
import nibabel as nib

mask = 
nib.load('/home/econdami/Desktop/test_resize/test_resizeNibabel/mask.nii')
ref = 
nib.load('/home/econdami/Desktop/test_resize/test_resizeNibabel/ref.nii')
ref3D = ref.slicer[:,:,:,0] # ref image data is 4-D array (length, 
length, length, time). Takes the first brain volume.
output=nibp.resample_from_to(mask, ref3D)
nib.save(output, 
'/home/econdami/Desktop/test_resize/test_resizeNibabel/output_image')


## *skimage.transform*

from skimage.transform import resize
import nibabel as nib

mask = nib.load('/home/econdami/Desktop/test_resize/test_skimage/mask.nii')
ref = nib.load('/home/econdami/Desktop/test_resize/test_skimage/ref.nii')
ref_data = ref.get_fdata()
mask_data = mask.get_fdata()
ref_size = ref_data.shape[:3] # ref image data is a 4-D array (length, 
length, length, time). Takes the first brain volume size.
output = resize(mask_data, ref_size, order=1, mode='reflect') # order=1 
(Bi-linear) is the default value and it seems that with 3D image, 
Bi-linear is equivalent to 'trilinear' of SPM's imcalc function ?
output_ref_mask = nib.Nifti1Image(output, ref.affine, mask.header) # 
Here some test was done by using also output_ref_ref = 
nib.Nifti1Image(output, ref.affine, ref.header) etc.
nib.save(output_ref_mask, 
'/home/econdami/Desktop/test_resize/test_skimage/output_image_ref_mask')

-------- Forwarded Message --------
Date: Fri, 11 Jan 2019 16:00:12 +0000
From: Matthew Brett <matthew.brett at gmail.com>
To: Neuroimaging analysis in Python <neuroimaging at python.org>
Subject: Re: [Neuroimaging] Apply resolution of one image.nii to another 
image.nii
Message-ID: 
<CAH6Pt5paJru9=XrUkH31tpN+zu9JqBD2Eb8xoR2urJdFn988Sg at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8

Hi,

Did you discover the processing module in nibabel? Maybe 
"resample_from_to" would help: 
http://nipy.org/nibabel/reference/nibabel.processing.html#nibabel.processing.resample_from_to

Something like: import nibabel.processing as nibp resized = 
nibp.resample_from_to(mask, ref)
Does that work? You'd probably have to threshold the image binarize it - 
trilinear resampling is the default - or use 0 (nearest neighbor) 
resampling.
Cheers, Matthew

-------- Forwarded Message --------
Subject: 	Re: [Neuroimaging] Apply resolution of one image.nii to 
another image.nii
Date: 	Fri, 11 Jan 2019 17:07:42 +0100 (CET)
From: 	Bertrand Thirion <bertrand.thirion at inria.fr>
To: 	eric.condamine at univ-grenoble-alpes.fr



Hi Eric,
you should use
nilearn.image.resample_to_img
Best,
Bertrand

------------------------------------------------------------------------

    *De: *"Eric Condamine" <eric.condamine at univ-grenoble-alpes.fr>
    *?: *neuroimaging at python.org
    *Envoy?: *Vendredi 11 Janvier 2019 16:26:05
    *Objet: *[Neuroimaging] Apply resolution of one image.nii to another
    image.nii

    Hello nipy experts,
    I would like to change the resolution of an nifti image (let's say
    mask.nii) according to the resolution of one other nifti image
    (let's say ref.nii), a process that i was doing with the imcalc
    function of spm before i start to switch to python ... i confess
    that i do not yet know all the tools currently available under nipy
    umbrella ...
    One way to do it could be something like that.

    """
    from skimage.transform import resize
    import nibabel as nib

    mask = nib.load(mask.nii)
    mask_data = mask.get_fdata()

    ref = nib.load(ref.nii)
    ref_data = ref.get_fdata()

    ref_size = ref_data.shape[:3]
    resized_mask_data = resize(mask_data, ref_size, order=1,
    mode='reflect') # order=1 (Bi-linear) is the default value and it
    seems that with 3D image, Bi-linear is equivalent to 'trilinear' of
    SPM's imcalc function ?

    mask_final = nib.Nifti1Image(resized_mask_data, xxx, yyy)
    nib.save(mask_final, mask_final)

    I do not succeed to obtain the wanted mask_final.nii (exactly the
    same as mask.nii, ie. same orientation in the same space, with only
    a change of the resolution). may be I am wrong with the xxx and yyy
    in nib.Nifti1Image().

    I tried:
    nib.Nifti1Image(resized_mask_data, mask.affine, ref.header)
    or
    nib.Nifti1Image(resized_mask_data, mask.affine, mask.header)
    etc. without success.

    So I plan to make a python function in order to make the correct
    header for the mask_final.nii after the resize() function.

    Because this need seems pretty commun, i guess that a tools to do it
    is is already existing in python ?

    So before reinvent the wheel, I would like to be sure that I do not
    make mistake with? xxx and/or yyy ?

    May be other function/tool doing the job and that I do not know? exist ?

    Thank you for all suggests or informations,

    All the best.
    -- 

    Eric Condamine  <http://fr.linkedin.com/pub/eric-condamine/27/529/290>

    IRMaGe  <https://irmage.ujf-grenoble.fr/>
    INSERM US17-CNRS UMS3552-UGA-CHUGA
    Unit? IRM 3T Recherche
    CHU Grenoble - CS 10217
    38043 Grenoble Cedex 9

    Tel : (00 33) 4 7676 7575 - Poste 63 202
         : (00 33) 4 7676 8726
    Fax : (00 33) 4 7676 9305
    e-mail:eric.condamine at univ-grenoble-alpes.fr  <eric.condamine at univ-grenoble-alpes.f>


    _______________________________________________
    Neuroimaging mailing list
    Neuroimaging at python.org
    https://mail.python.org/mailman/listinfo/neuroimaging

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From h.benoudjit at gmail.com  Sat Jan 19 20:48:44 2019
From: h.benoudjit at gmail.com (Hakim Benoudjit)
Date: Sun, 20 Jan 2019 01:48:44 +0000
Subject: [Neuroimaging] MRF segmentation on a single-band image
Message-ID: <CAC0V5F9ozHOJ8hmVnQBHaawvxZmzxfvz81rnKg6ogazT_3erUQ@mail.gmail.com>

Hi,

I've installed nipy to try out the MRF segmentation included with it. The
issue for me is that my dataset contains images with a single-band
(gray-level in float), which are not really medical images (remote sensing
images instead).

I was wondering why the Segmentation algorithm works only with images with
3 or 4 bands?
I'm alluding to this line in the source-code:
https://github.com/nipy/nipy/blob/628ad8dc41dc0d0a113dcf59ee5921348377b942/nipy/algorithms/segmentation/segmentation.py#L47

Thanks.

Hakim.
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From greynell at gmail.com  Wed Jan 23 06:05:37 2019
From: greynell at gmail.com (=?UTF-8?Q?Gabriel_Reyn=C3=A9s?=)
Date: Wed, 23 Jan 2019 12:05:37 +0100
Subject: [Neuroimaging] Image reslicing
Message-ID: <CADbFBMF4bPQayW5ZzZjnk0zFAw4iBQsQ6mM54o_buc_TWUAXGg@mail.gmail.com>

Dear experts,


I am doing an small project on Dynamic Susceptibility Contrast (DSC-PWI)
MRI, I am trying to

So, I have a T1 of  shape (256, 256, 20) and a DSC of shape (128, 128, 30).
Both images are corregistred.
I want to extract the white matter of the T1 to use it as a mask for the
DSC image, but I am stuck in a very initial phase.
To do so I need to reslice the T1 to the DSC MRI, and I am using the
reslice function of dipy:
reslicedT1, affine2 = reslice(T1_im_data, T1_affine, T1_zooms,DSC_zooms)

where DSC_zooms are the zoom extracted from the nii header. The problem in
doing so is that the final shape obtaned is (134, 134, 38). What I am
missing?



Thanks

Gabriel
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From arokem at gmail.com  Thu Jan 24 18:07:26 2019
From: arokem at gmail.com (Ariel Rokem)
Date: Thu, 24 Jan 2019 15:07:26 -0800
Subject: [Neuroimaging] Postdoc positions in the Yeatman Lab (University of
 Washington, Seattle)
Message-ID: <CA+X4w0wkBK97w644hausXxHcxzY5uOqjQFapGVrr+_nsc9MMSg@mail.gmail.com>

Excellent opportunity for post-doctoral training at the University of
Washington, on a range of different projects (some in collaboration with
yours truly).

See:
http://depts.washington.edu/bdelab/2018/12/17/postdoc-position-neurobiology-reading-dyslexia/,
or attached flier.

Cheers,

Ariel
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From federico.nemmi at gmail.com  Thu Jan 31 05:38:55 2019
From: federico.nemmi at gmail.com (federico nemmi)
Date: Thu, 31 Jan 2019 11:38:55 +0100
Subject: [Neuroimaging] chainging sform and save back image
Message-ID: <CA+UmSvLCwKBGXTWY5Cd--E+7OFHBODkzHNrBiyQ=bJ7K4xeDZA@mail.gmail.com>

Hi everyone,
I am trying to change the sform of an image to those of another image and
save the first image back as a nifti file.
To do so I do something in the line of
> import nipy as ni
> img_to_change = ni.load_image("my_image_to_change.nii")
> ref_image = ni.load_image("my_ref_image.nii")
>  img_to_change .metadata["header"]["sform_code"]  = ref_image
.metadata["header"]["sform_code"]

When I wheck now the value of the sform code for the first image it is
indeed equal to the value of the sform code in the reference image.
However, if I now save the first image with

>ni.save_image(img_to_change, "modified_img.nii")

load it back

>new_img = ni.load_image("modified_img.nii")

and check the sform code, this is as in the original image !

Am I missing something, is there a step that I skipping between changing
the header of the first image and save it ?
Thank in advance

F.
-- 
Federico Nemmi, PhD
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From 20100thomas at gmail.com  Thu Jan 31 06:22:18 2019
From: 20100thomas at gmail.com (Thomas Vincent)
Date: Thu, 31 Jan 2019 06:22:18 -0500
Subject: [Neuroimaging] chainging sform and save back image
In-Reply-To: <CA+UmSvLCwKBGXTWY5Cd--E+7OFHBODkzHNrBiyQ=bJ7K4xeDZA@mail.gmail.com>
References: <CA+UmSvLCwKBGXTWY5Cd--E+7OFHBODkzHNrBiyQ=bJ7K4xeDZA@mail.gmail.com>
Message-ID: <CAMjNW7_9MPTUwoVYMs_TD3CftpNHZTxJhVgrCXK-ZEAM8UmWWA@mail.gmail.com>

I think the sform is adapted when saving to maintain some consistency with
other fields.

The easiest way to make it work is to copy the data from img_to_change into
ref_image and then save ref_image to a new file.

Thomas.


Le jeu. 31 janv. 2019 05 h 39, federico nemmi <federico.nemmi at gmail.com> a
?crit :

> Hi everyone,
> I am trying to change the sform of an image to those of another image and
> save the first image back as a nifti file.
> To do so I do something in the line of
> > import nipy as ni
> > img_to_change = ni.load_image("my_image_to_change.nii")
> > ref_image = ni.load_image("my_ref_image.nii")
> >  img_to_change .metadata["header"]["sform_code"]  = ref_image
> .metadata["header"]["sform_code"]
>
> When I wheck now the value of the sform code for the first image it is
> indeed equal to the value of the sform code in the reference image.
> However, if I now save the first image with
>
> >ni.save_image(img_to_change, "modified_img.nii")
>
> load it back
>
> >new_img = ni.load_image("modified_img.nii")
>
> and check the sform code, this is as in the original image !
>
> Am I missing something, is there a step that I skipping between changing
> the header of the first image and save it ?
> Thank in advance
>
> F.
> --
> Federico Nemmi, PhD
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From federico.nemmi at gmail.com  Thu Jan 31 07:11:59 2019
From: federico.nemmi at gmail.com (federico nemmi)
Date: Thu, 31 Jan 2019 13:11:59 +0100
Subject: [Neuroimaging] chainging sform and save back image
In-Reply-To: <CAMjNW7_9MPTUwoVYMs_TD3CftpNHZTxJhVgrCXK-ZEAM8UmWWA@mail.gmail.com>
References: <CA+UmSvLCwKBGXTWY5Cd--E+7OFHBODkzHNrBiyQ=bJ7K4xeDZA@mail.gmail.com>
 <CAMjNW7_9MPTUwoVYMs_TD3CftpNHZTxJhVgrCXK-ZEAM8UmWWA@mail.gmail.com>
Message-ID: <CA+UmSvJ1Bo2BQ4PraaD45e5bUJ-WGp+yUeXVfjxTEigRFZSQ6w@mail.gmail.com>

Sounds reasonable. I'll give it a try!
F.

Il giorno gio 31 gen 2019 alle ore 12:22 Thomas Vincent <
20100thomas at gmail.com> ha scritto:

> I think the sform is adapted when saving to maintain some consistency with
> other fields.
>
> The easiest way to make it work is to copy the data from img_to_change
> into ref_image and then save ref_image to a new file.
>
> Thomas.
>
>
> Le jeu. 31 janv. 2019 05 h 39, federico nemmi <federico.nemmi at gmail.com>
> a ?crit :
>
>> Hi everyone,
>> I am trying to change the sform of an image to those of another image and
>> save the first image back as a nifti file.
>> To do so I do something in the line of
>> > import nipy as ni
>> > img_to_change = ni.load_image("my_image_to_change.nii")
>> > ref_image = ni.load_image("my_ref_image.nii")
>> >  img_to_change .metadata["header"]["sform_code"]  = ref_image
>> .metadata["header"]["sform_code"]
>>
>> When I wheck now the value of the sform code for the first image it is
>> indeed equal to the value of the sform code in the reference image.
>> However, if I now save the first image with
>>
>> >ni.save_image(img_to_change, "modified_img.nii")
>>
>> load it back
>>
>> >new_img = ni.load_image("modified_img.nii")
>>
>> and check the sform code, this is as in the original image !
>>
>> Am I missing something, is there a step that I skipping between changing
>> the header of the first image and save it ?
>> Thank in advance
>>
>> F.
>> --
>> Federico Nemmi, PhD
>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>


-- 
Federico Nemmi, PhD
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From arnaud.bore at gmail.com  Thu Jan 31 09:07:09 2019
From: arnaud.bore at gmail.com (=?UTF-8?B?QXJuYXVkIEJvcsOp?=)
Date: Thu, 31 Jan 2019 09:07:09 -0500
Subject: [Neuroimaging] Research assistant position in Dr Doyon lab (McGill
 University, Montreal, QC, CA)
Message-ID: <CAPA8YjbFrG2iLRpSAt074WJ69-Tw7cdo6zMXCPr=g_KheyCuBA@mail.gmail.com>

Position Title:  Research Assistant
Hiring Unit: ?  McConnell Brain Imaging Centre ? Montreal Neurological
Institute
Supervisor:  Dr. Julien Doyon
Work Location:  3801 University, Montreal Neurological Institute
Hours/Week & Schedule:  35 hours/week; 9:00 ? 5:00 ? Monday to Friday
Hourly Wage:  $27.87/hour (salary commensurate with experience)
Planned Start  Date & End Date:  ASAP ? one year (renewable)
Deadline to Apply:  February 8, 2019

*PRIMARY DUTIES *
We are looking to hire a research assistant to provide support to the
supervisor  for all ongoing
research projects . Assist graduate students and postdoctoral fellows in
carrying out behavioral and neuroimaging studies in cognitive neuroscience,
and motor learning in particular. Develop, oversee and maintain data
analysis pipelines in conjunction with graduate students and postdoctoral
fellows. Supervise undergraduate students as well as casuals.


*EDUCATION/EXPERIENCE*
MSc degree in computer science or neuroscience with a strong coding
experience in Matlab and Python applied to neurosciences.


*OTHER QUALIFYING SKILLS & ABILITIES*

   - Good proficiency using Matlab and coding in Python in neurosciences
   (preferably in human brain imaging);
   - Knowledge of neuroimaging software such as FreeSurfer, FSL, AFNI or
   SPM.
   - Good communications skills in French or English (both ? preferred).
   - Social and interpersonal skills.
   - Team player and dedication to the work at hand.
   - Ability to work autonomously and deliver on set deadlines.
   - Willingness to learn new imaging and data analysis techniques.
   - Experience in neurosciences research, preferably in brain and/or
   spinal cord imaging and a good understanding of statistical analysis
   pertaining to neuroimaging data will be an asset.

*HOW TO APPLY*
Please submit your application to: Dr Julien Doyon by email
*julien.doyon at mcgill.ca <julien.doyon at mcgill.ca>    *

*McGill University is committed to equity in employment and diversity. It
welcomes applications from indigenous peoples, **visible minorities, ethnic
minorities, persons with disabilities, women, persons of minority sexual
orientations and gender **identities, and others who may contribute to
further diversification. *
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From matthew.brett at gmail.com  Thu Jan 31 12:55:24 2019
From: matthew.brett at gmail.com (Matthew Brett)
Date: Thu, 31 Jan 2019 17:55:24 +0000
Subject: [Neuroimaging] Chris Markiewicz taking over as lead maintainer for
 nibabel
Message-ID: <CAH6Pt5rBgHn8rMW-UsLEd9N_6F-MfPYPr6a=rq_X5Q2w1TuH0g@mail.gmail.com>

Hi,

Just so y'all know, Chris has kindly agreed to take over the role of
lead maintainer for nibabel.

Well, I should say, he had kindly agreed to take on the title, because
the observant among you will know he has effectively been doing that
job for some time.

We nibabelers don't have any real governance docs, but, as my last act
as lead maintainer, I'm going propose the following:

* the lead maintainer has veto power over commits to nibabel
* they should use it only very rarely, when all possible compromises
have been explored.

If anyone disagrees with this little formalization, please do say.

Thanks very much, as ever, to Chris, and good luck with the task, that
you are already doing...

Cheers,

Matthew

From krzysztof.gorgolewski at gmail.com  Thu Jan 31 12:59:07 2019
From: krzysztof.gorgolewski at gmail.com (Chris Gorgolewski)
Date: Thu, 31 Jan 2019 09:59:07 -0800
Subject: [Neuroimaging] Chris Markiewicz taking over as lead maintainer
 for nibabel
In-Reply-To: <CAH6Pt5rBgHn8rMW-UsLEd9N_6F-MfPYPr6a=rq_X5Q2w1TuH0g@mail.gmail.com>
References: <CAH6Pt5rBgHn8rMW-UsLEd9N_6F-MfPYPr6a=rq_X5Q2w1TuH0g@mail.gmail.com>
Message-ID: <CAAQzouP191h8L+WSwNMVmFAjQkBDEO1Z7n+gLVKd1eNW5DmPhg@mail.gmail.com>

Congratulations to Chris and many thanks for years of extremely valuable
service both of you provided to the community.

Best,
Chris


On Thu, Jan 31, 2019 at 9:56 AM Matthew Brett <matthew.brett at gmail.com>
wrote:

> Hi,
>
> Just so y'all know, Chris has kindly agreed to take over the role of
> lead maintainer for nibabel.
>
> Well, I should say, he had kindly agreed to take on the title, because
> the observant among you will know he has effectively been doing that
> job for some time.
>
> We nibabelers don't have any real governance docs, but, as my last act
> as lead maintainer, I'm going propose the following:
>
> * the lead maintainer has veto power over commits to nibabel
> * they should use it only very rarely, when all possible compromises
> have been explored.
>
> If anyone disagrees with this little formalization, please do say.
>
> Thanks very much, as ever, to Chris, and good luck with the task, that
> you are already doing...
>
> Cheers,
>
> Matthew
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From gael.varoquaux at normalesup.org  Thu Jan 31 13:01:56 2019
From: gael.varoquaux at normalesup.org (Gael Varoquaux)
Date: Thu, 31 Jan 2019 19:01:56 +0100
Subject: [Neuroimaging] Chris Markiewicz taking over as lead maintainer
 for nibabel
In-Reply-To: <CAH6Pt5rBgHn8rMW-UsLEd9N_6F-MfPYPr6a=rq_X5Q2w1TuH0g@mail.gmail.com>
References: <CAH6Pt5rBgHn8rMW-UsLEd9N_6F-MfPYPr6a=rq_X5Q2w1TuH0g@mail.gmail.com>
Message-ID: <20190131180156.gofsraum23fzvhfh@phare.normalesup.org>

Thanks Matthew for all the work for many many years. I hope that you feel
the impact of what you have created: there is a thriving community of
happy Python neuroimagers, which is rapidly growing.

Cheers,

Ga?l

On Thu, Jan 31, 2019 at 05:55:24PM +0000, Matthew Brett wrote:
> Hi,

> Just so y'all know, Chris has kindly agreed to take over the role of
> lead maintainer for nibabel.

> Well, I should say, he had kindly agreed to take on the title, because
> the observant among you will know he has effectively been doing that
> job for some time.

> We nibabelers don't have any real governance docs, but, as my last act
> as lead maintainer, I'm going propose the following:

> * the lead maintainer has veto power over commits to nibabel
> * they should use it only very rarely, when all possible compromises
> have been explored.

> If anyone disagrees with this little formalization, please do say.

> Thanks very much, as ever, to Chris, and good luck with the task, that
> you are already doing...

> Cheers,

> Matthew
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging

-- 
    Gael Varoquaux
    Senior Researcher, INRIA Parietal
    NeuroSpin/CEA Saclay , Bat 145, 91191 Gif-sur-Yvette France
    Phone:  ++ 33-1-69-08-79-68
    http://gael-varoquaux.info            http://twitter.com/GaelVaroquaux

From matthew.brett at gmail.com  Thu Jan 31 13:04:04 2019
From: matthew.brett at gmail.com (Matthew Brett)
Date: Thu, 31 Jan 2019 18:04:04 +0000
Subject: [Neuroimaging] Chris Markiewicz taking over as lead maintainer
 for nibabel
In-Reply-To: <20190131180156.gofsraum23fzvhfh@phare.normalesup.org>
References: <CAH6Pt5rBgHn8rMW-UsLEd9N_6F-MfPYPr6a=rq_X5Q2w1TuH0g@mail.gmail.com>
 <20190131180156.gofsraum23fzvhfh@phare.normalesup.org>
Message-ID: <CAH6Pt5rKO-bPj_HsnEkr5QEmQMG1WAB3pNhZp2b_kVBR6h1YRA@mail.gmail.com>

Hi,

On Thu, Jan 31, 2019 at 6:02 PM Gael Varoquaux
<gael.varoquaux at normalesup.org> wrote:
>
> Thanks Matthew for all the work for many many years. I hope that you feel
> the impact of what you have created: there is a thriving community of
> happy Python neuroimagers, which is rapidly growing.

Oh yes - I do feel that - and that there are many sturdy shoulders
pushing the wheel, so thanks right back at you.

Cheers,

Matthew

From gael.varoquaux at normalesup.org  Thu Jan 31 13:10:46 2019
From: gael.varoquaux at normalesup.org (Gael Varoquaux)
Date: Thu, 31 Jan 2019 19:10:46 +0100
Subject: [Neuroimaging] Chris Markiewicz taking over as lead maintainer
 for nibabel
In-Reply-To: <CAH6Pt5rKO-bPj_HsnEkr5QEmQMG1WAB3pNhZp2b_kVBR6h1YRA@mail.gmail.com>
References: <CAH6Pt5rBgHn8rMW-UsLEd9N_6F-MfPYPr6a=rq_X5Q2w1TuH0g@mail.gmail.com>
 <20190131180156.gofsraum23fzvhfh@phare.normalesup.org>
 <CAH6Pt5rKO-bPj_HsnEkr5QEmQMG1WAB3pNhZp2b_kVBR6h1YRA@mail.gmail.com>
Message-ID: <20190131181046.2sz7vg4cwrapwk53@phare.normalesup.org>

On Thu, Jan 31, 2019 at 06:04:04PM +0000, Matthew Brett wrote:
> Oh yes - I do feel that - and that there are many sturdy shoulders
> pushing the wheel, so thanks right back at you.

I haven't done anything for nibabel in many years, though I am an avid
user. The nibabel developers are the giants on which shoulders the
neuromaging world standards.

Ga?l

From bertrand.thirion at inria.fr  Thu Jan 31 13:28:08 2019
From: bertrand.thirion at inria.fr (Bertrand Thirion)
Date: Thu, 31 Jan 2019 19:28:08 +0100 (CET)
Subject: [Neuroimaging] Chris Markiewicz taking over as lead maintainer
 for nibabel
In-Reply-To: <20190131180156.gofsraum23fzvhfh@phare.normalesup.org>
References: <CAH6Pt5rBgHn8rMW-UsLEd9N_6F-MfPYPr6a=rq_X5Q2w1TuH0g@mail.gmail.com>
 <20190131180156.gofsraum23fzvhfh@phare.normalesup.org>
Message-ID: <205638348.3667315.1548959288689.JavaMail.zimbra@inria.fr>

Indeed, big thanks to Chris, Matthew and all nibabel developers !
Cheers,
Bertrand

----- Mail original -----
> De: "Gael Varoquaux" <gael.varoquaux at normalesup.org>
> ?: "Neuroimaging analysis in Python" <neuroimaging at python.org>
> Envoy?: Jeudi 31 Janvier 2019 19:01:56
> Objet: Re: [Neuroimaging] Chris Markiewicz taking over as lead maintainer for nibabel

> Thanks Matthew for all the work for many many years. I hope that you feel
> the impact of what you have created: there is a thriving community of
> happy Python neuroimagers, which is rapidly growing.
> 
> Cheers,
> 
> Ga?l
> 
> On Thu, Jan 31, 2019 at 05:55:24PM +0000, Matthew Brett wrote:
>> Hi,
> 
>> Just so y'all know, Chris has kindly agreed to take over the role of
>> lead maintainer for nibabel.
> 
>> Well, I should say, he had kindly agreed to take on the title, because
>> the observant among you will know he has effectively been doing that
>> job for some time.
> 
>> We nibabelers don't have any real governance docs, but, as my last act
>> as lead maintainer, I'm going propose the following:
> 
>> * the lead maintainer has veto power over commits to nibabel
>> * they should use it only very rarely, when all possible compromises
>> have been explored.
> 
>> If anyone disagrees with this little formalization, please do say.
> 
>> Thanks very much, as ever, to Chris, and good luck with the task, that
>> you are already doing...
> 
>> Cheers,
> 
>> Matthew
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
> 
> --
>    Gael Varoquaux
>    Senior Researcher, INRIA Parietal
>    NeuroSpin/CEA Saclay , Bat 145, 91191 Gif-sur-Yvette France
>    Phone:  ++ 33-1-69-08-79-68
>    http://gael-varoquaux.info            http://twitter.com/GaelVaroquaux
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging

From njvack at wisc.edu  Thu Jan 31 14:49:04 2019
From: njvack at wisc.edu (Nate Vack)
Date: Thu, 31 Jan 2019 13:49:04 -0600
Subject: [Neuroimaging] Chris Markiewicz taking over as lead maintainer
 for nibabel
In-Reply-To: <11760_1548959514_0PM700HM3KSMP140_205638348.3667315.1548959288689.JavaMail.zimbra@inria.fr>
References: <CAH6Pt5rBgHn8rMW-UsLEd9N_6F-MfPYPr6a=rq_X5Q2w1TuH0g@mail.gmail.com>
 <20190131180156.gofsraum23fzvhfh@phare.normalesup.org>
 <11760_1548959514_0PM700HM3KSMP140_205638348.3667315.1548959288689.JavaMail.zimbra@inria.fr>
Message-ID: <CA+1BpOsJBapvHa-AtHHc04BVm2QcObxcrkT6P2R7+J9sKF0JCQ@mail.gmail.com>

That is excellent news! Thank you for making and supporting nibabel; it is
insanely useful.

Best,
-Nate
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From lists at onerussian.com  Thu Jan 31 16:20:36 2019
From: lists at onerussian.com (Yaroslav Halchenko)
Date: Thu, 31 Jan 2019 16:20:36 -0500
Subject: [Neuroimaging] Chris Markiewicz taking over as lead maintainer
 for nibabel
In-Reply-To: <CAH6Pt5rBgHn8rMW-UsLEd9N_6F-MfPYPr6a=rq_X5Q2w1TuH0g@mail.gmail.com>
References: <CAH6Pt5rBgHn8rMW-UsLEd9N_6F-MfPYPr6a=rq_X5Q2w1TuH0g@mail.gmail.com>
Message-ID: <20190131212036.GZ3725@hopa.kiewit.dartmouth.edu>


On Thu, 31 Jan 2019, Matthew Brett wrote:

> Well, I should say, he had kindly agreed to take on the title, because
> the observant among you will know he has effectively been doing that
> job for some time.

Dear Matthew,  thank you for all hard work and wise guidance in the
past, and I still hope to meet you again sometime/somewhere.


> We nibabelers don't have any real governance docs, but, as my last act
> as lead maintainer, I'm going propose the following:

> * the lead maintainer has veto power over commits to nibabel
> * they should use it only very rarely, when all possible compromises
> have been explored.

It is great to see it being Chris to carry this burden, so whenever all
other means are explored/exploited, I could just drive 40 minutes south,
drag him out for a pint, and  reach the only possible correct
decision ;)

Cheers,
-- 
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik        

From jbpoline at gmail.com  Thu Jan 31 17:27:07 2019
From: jbpoline at gmail.com (JB Poline)
Date: Thu, 31 Jan 2019 17:27:07 -0500
Subject: [Neuroimaging] Chris Markiewicz taking over as lead maintainer
 for nibabel
In-Reply-To: <20190131212036.GZ3725@hopa.kiewit.dartmouth.edu>
References: <CAH6Pt5rBgHn8rMW-UsLEd9N_6F-MfPYPr6a=rq_X5Q2w1TuH0g@mail.gmail.com>
 <20190131212036.GZ3725@hopa.kiewit.dartmouth.edu>
Message-ID: <CALMaa83i5viGt9sS_nm6eyotB4i64kxwJyVsYmWR-0T9BXpPTg@mail.gmail.com>

beer decision making sounds great :)
+1 on the super useful work that Matthew put in nibabel...

On Thu, Jan 31, 2019 at 4:50 PM Yaroslav Halchenko <lists at onerussian.com>
wrote:

>
> On Thu, 31 Jan 2019, Matthew Brett wrote:
>
> > Well, I should say, he had kindly agreed to take on the title, because
> > the observant among you will know he has effectively been doing that
> > job for some time.
>
> Dear Matthew,  thank you for all hard work and wise guidance in the
> past, and I still hope to meet you again sometime/somewhere.
>
>
> > We nibabelers don't have any real governance docs, but, as my last act
> > as lead maintainer, I'm going propose the following:
>
> > * the lead maintainer has veto power over commits to nibabel
> > * they should use it only very rarely, when all possible compromises
> > have been explored.
>
> It is great to see it being Chris to carry this burden, so whenever all
> other means are explored/exploited, I could just drive 40 minutes south,
> drag him out for a pint, and  reach the only possible correct
> decision ;)
>
> Cheers,
> --
> Yaroslav O. Halchenko
> Center for Open Neuroscience     http://centerforopenneuroscience.org
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
> WWW:   http://www.linkedin.com/in/yarik
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From satra at mit.edu  Thu Jan 31 18:46:43 2019
From: satra at mit.edu (Satrajit Ghosh)
Date: Thu, 31 Jan 2019 18:46:43 -0500
Subject: [Neuroimaging] Chris Markiewicz taking over as lead maintainer
 for nibabel
In-Reply-To: <CAH6Pt5rBgHn8rMW-UsLEd9N_6F-MfPYPr6a=rq_X5Q2w1TuH0g@mail.gmail.com>
References: <CAH6Pt5rBgHn8rMW-UsLEd9N_6F-MfPYPr6a=rq_X5Q2w1TuH0g@mail.gmail.com>
Message-ID: <CA+A4wOmpnC=ygeEmMEcb90BYn_+wFzXnosxA_7acjTrb-YFc4A@mail.gmail.com>

thank you very much matthew for all the shepherding over the years. and
chris for taking over and making seem seamless the reviews, the
discussions, and the maintenance, not just of nibabel but the many projects
you take care of.

it's been incredible to be part of such a giving community.

cheers,

satra

On Thu, Jan 31, 2019 at 12:56 PM Matthew Brett <matthew.brett at gmail.com>
wrote:

> Hi,
>
> Just so y'all know, Chris has kindly agreed to take over the role of
> lead maintainer for nibabel.
>
> Well, I should say, he had kindly agreed to take on the title, because
> the observant among you will know he has effectively been doing that
> job for some time.
>
> We nibabelers don't have any real governance docs, but, as my last act
> as lead maintainer, I'm going propose the following:
>
> * the lead maintainer has veto power over commits to nibabel
> * they should use it only very rarely, when all possible compromises
> have been explored.
>
> If anyone disagrees with this little formalization, please do say.
>
> Thanks very much, as ever, to Chris, and good luck with the task, that
> you are already doing...
>
> Cheers,
>
> Matthew
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From code at oscaresteban.es  Thu Jan 31 19:06:08 2019
From: code at oscaresteban.es (Oscar Esteban)
Date: Thu, 31 Jan 2019 16:06:08 -0800
Subject: [Neuroimaging] Chris Markiewicz taking over as lead maintainer
 for nibabel
In-Reply-To: <CA+A4wOmpnC=ygeEmMEcb90BYn_+wFzXnosxA_7acjTrb-YFc4A@mail.gmail.com>
References: <CAH6Pt5rBgHn8rMW-UsLEd9N_6F-MfPYPr6a=rq_X5Q2w1TuH0g@mail.gmail.com>
 <CA+A4wOmpnC=ygeEmMEcb90BYn_+wFzXnosxA_7acjTrb-YFc4A@mail.gmail.com>
Message-ID: <CAAsFcgwQW-EJtS09Q496WOScst53hwQjYoOO5XN5vzexiWCgnQ@mail.gmail.com>

Thanks very much, Matthew. Your driving of nibabel through these years has
made it the cornerstone of neuroimaging, and one of the most robust pieces
of software available to this community.

Congrats Chris, I'm sure you'll keep up the good work :)

Cheers,
Oscar


On Thu, Jan 31, 2019 at 3:47 PM Satrajit Ghosh <satra at mit.edu> wrote:

> thank you very much matthew for all the shepherding over the years. and
> chris for taking over and making seem seamless the reviews, the
> discussions, and the maintenance, not just of nibabel but the many projects
> you take care of.
>
> it's been incredible to be part of such a giving community.
>
> cheers,
>
> satra
>
> On Thu, Jan 31, 2019 at 12:56 PM Matthew Brett <matthew.brett at gmail.com>
> wrote:
>
>> Hi,
>>
>> Just so y'all know, Chris has kindly agreed to take over the role of
>> lead maintainer for nibabel.
>>
>> Well, I should say, he had kindly agreed to take on the title, because
>> the observant among you will know he has effectively been doing that
>> job for some time.
>>
>> We nibabelers don't have any real governance docs, but, as my last act
>> as lead maintainer, I'm going propose the following:
>>
>> * the lead maintainer has veto power over commits to nibabel
>> * they should use it only very rarely, when all possible compromises
>> have been explored.
>>
>> If anyone disagrees with this little formalization, please do say.
>>
>> Thanks very much, as ever, to Chris, and good luck with the task, that
>> you are already doing...
>>
>> Cheers,
>>
>> Matthew
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From markiewicz at stanford.edu  Thu Jan 31 21:42:49 2019
From: markiewicz at stanford.edu (Christopher Markiewicz)
Date: Fri, 1 Feb 2019 02:42:49 +0000
Subject: [Neuroimaging] Chris Markiewicz taking over as lead maintainer
 for nibabel
In-Reply-To: <CAH6Pt5rBgHn8rMW-UsLEd9N_6F-MfPYPr6a=rq_X5Q2w1TuH0g@mail.gmail.com>
References: <CAH6Pt5rBgHn8rMW-UsLEd9N_6F-MfPYPr6a=rq_X5Q2w1TuH0g@mail.gmail.com>
Message-ID: <BN6PR02MB2675135BCB29F2AE301BED9CA9920@BN6PR02MB2675.namprd02.prod.outlook.com>

Thanks, Matthew, for your many years of guidance and support of nibabel and its contributors. I credit my engagement with nibabel in particular with teaching me how to write and maintain open source software, and I can only say thank you. It really is the bedrock of the community, and I hope to keep it in worthy shape.

Chris


________________________________
From: Neuroimaging <neuroimaging-bounces+markiewicz=stanford.edu at python.org> on behalf of Matthew Brett <matthew.brett at gmail.com>
Sent: Thursday, January 31, 2019 12:55 PM
To: neuroimaging
Subject: [Neuroimaging] Chris Markiewicz taking over as lead maintainer for nibabel

Hi,

Just so y'all know, Chris has kindly agreed to take over the role of
lead maintainer for nibabel.

Well, I should say, he had kindly agreed to take on the title, because
the observant among you will know he has effectively been doing that
job for some time.

We nibabelers don't have any real governance docs, but, as my last act
as lead maintainer, I'm going propose the following:

* the lead maintainer has veto power over commits to nibabel
* they should use it only very rarely, when all possible compromises
have been explored.

If anyone disagrees with this little formalization, please do say.

Thanks very much, as ever, to Chris, and good luck with the task, that
you are already doing...

Cheers,

Matthew
_______________________________________________
Neuroimaging mailing list
Neuroimaging at python.org
https://mail.python.org/mailman/listinfo/neuroimaging
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