[Neuroimaging] failure using DIPY Free Water Elimination DTI

Ping-Hong Yeh pinghongyeh at gmail.com
Sat Jan 12 16:17:05 EST 2019 

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
>>>>>>>>>
>>>>>>>>> _______________________________________________
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>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>
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