[Neuroimaging] failure using DIPY Free Water Elimination DTI

[Ariel Rokem]

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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/neuroimaging/attachments/20190104/678f9328/attachment.html>