[Mrtrix-discussion] nipype issue

[J-Donald Tournier]

Hi,

I'm afraid I have to idea about nipype... My only guess is that the MRtrix
commands need to be available in your PATH, but that's just a guess. Your
best bet is to contact the nipype people...

Cheers,
Donald.


On 16 December 2014 at 17:37, anvi vora <anvikvora at gmail.com> wrote:
>
> Hello,
>
> I am attempting to run a pipeline from nipype which wraps mrtrix.
>
> It is the script called dmri_mrtrix_dti
>
> I have installed the mrtrix and compiled it successfully for my macbook.
>
> I get the following error, which seems to indicate that I do not have all
> the required binaries:  I looked and I couldn't find these commands in bin
> folder.  Any help is appreciated!!! Thank you
>
> ERROR:workflow:could not run node: dwiproc.tractography.tensor2fa.a0
> INFO:workflow:crashfile: /Users/macbook/Desktop/crash-20141215-235215-macbook-tensor2fa.a0.npz
> ERROR:workflow:could not run node: dwiproc.tractography.tensor2adc.a0
> INFO:workflow:crashfile: /Users/macbook/Desktop/crash-20141215-235215-macbook-tensor2adc.a0.npz
> ERROR:workflow:could not run node: dwiproc.tractography.tensor2vector.a0
> INFO:workflow:crashfile: /Users/macbook/Desktop/crash-20141215-235215-macbook-tensor2vector.a0.npz
> ERROR:workflow:could not run node: dwiproc.tractography.gen_WM_mask.a0
> INFO:workflow:crashfile: /Users/macbook/Desktop/crash-20141215-235215-macbook-gen_WM_mask.a0.npz
> ERROR:workflow:could not run node: dwiproc.tractography.threshold_b0.a0
> INFO:workflow:crashfile: /Users/macbook/Desktop/crash-20141215-235215-macbook-threshold_b0.a0.npz
> INFO:workflow:***********************************
>
>
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>

-- 
*Dr J-Donald Tournier (PhD)*

*Senior Lecturer, **Biomedical Engineering*

*Division of Imaging Sciences & Biomedical EngineeringKing's College London*


*A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
Thomas' Hospital, London. SE1 7EH*
*T: +44 (0)20 7188 7118 ext 53613*
*W: http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
<http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering>*
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