Hi Saad,
Thanks a lot, it works now.
Best,
Martin
On 03/24/14 13:54, Saad Jbabdi wrote:
> Hi
>
> There are several things you need to do:
> - change the output directory name according to e.g. the name of your
> seed file (otherwise all the jobs will attempt to write in the same
> directory)
> - add the --os2t option
> - you can also use --s2tastext if you want to get the results as ASCII file
>
> Cheers
> saad
>
> On 24 Mar 2014, at 17:03, Martin Luessi <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
>> Dear FSL experts,
>>
>> I'm trying to use probtrackx2 to compute N x N connectivity between N
>> binary masks defined in diffusion space. To speed things up, I would
>> like to run it in parallel using 1 seed at a time. I tried is the
>> following
>>
>> probtrackx2 -s /Diffusion.bedpostX/merged \
>> -m /Diffusion/nodif_brain_mask.nii.gz \
>> -x /seed1_mask.nii.gz \
>> --targetmasks=/tmp/dsi_targets.txt
>>
>> where dsi_targets.txt is a text file with one filename per line for each
>> target mask (which are in .nii.gz format). When I ran probtrackx2 using
>> the options above, it created a "logdir" with 5000 empty files, so I
>> assume I must be doing something wrong. Is there a way to run
>> probtrackx2 to directly output an "1 x N" matrix, i.e., one count for
>> each mask in "dsi"targets.txt"?
>>
>> Best,
>>
>> Martin
>>
>>
>>
>>
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> --
> Saad Jbabdi
> University of Oxford, FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> (+44)1865-222466 (fax 717)
> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
> <http://www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi>
>
--
Martin Luessi, Ph.D.
Research Fellow
Department of Radiology
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Harvard Medical School
149 13th Street
Charlestown, MA 02129
Fax: +1 617 726-7422
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