[Mrtrix-discussion] nipype issue
Ariel Rokem
arokem at gmail.com
Wed Dec 17 09:48:51 PST 2014
Redirecting to the nipy-user mailing list (see below):
On Wed, Dec 17, 2014 at 5:40 AM, J-Donald Tournier <jdtournier at gmail.com>
wrote:
>
> 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:***********************************
>>
>>
>> _______________________________________________
>> Mrtrix-discussion mailing list
>> Mrtrix-discussion at www.nitrc.org
>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>
>>
>
> --
> *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
> <%2B44%20%280%2920%207188%207118%20ext%2053613>*
> *W: http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
> <http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering>*
>
> _______________________________________________
> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.nitrc.org/pipermail/mrtrix-discussion/attachments/20141217/980e5a38/attachment.html>
More information about the Mrtrix-discussion
mailing list