Did you use the surfaces in ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k
and is your diffusion data in ${StudyFolder}/${Subject}/T1w/Diffusion?
The metric file should be able to be displayed on the same surfaces you
use for tractography. Here is code that I use for the conversions:
if [ $MatrixNumber = "1" ] ; then
MakeSymmetric=""
elif [ $MatrixNumber = "3" ] ; then
MakeSymmetric="-make-symmetric"
fi
Dir="${ResultsFolder}/${Hemisphere}_Trajectory_Matrix${MatrixNumber}${PDDir
}_${StepSize}"
$Caret7_Command -probtrackx-dot-convert
${Dir}/fdt_matrix${MatrixNumber}.dot
${Dir}/fdt_matrix"$MatrixNumber".dconn.nii -row-surface
${Dir}/SeedSpaceMetric.func.gii -col-surface
${Dir}/SeedSpaceMetric.func.gii -transpose ${MakeSymmetric}
$Caret7_Command -convert-matrix4-to-workbench-sparse
${Dir}/fdt_matrix4_1.mtx ${Dir}/fdt_matrix4_2.mtx ${Dir}/fdt_matrix4_3.mtx
${BedpostXFolder}/Whole_Brain_Trajectory_${DiffusionResolution}.fiberTEMP.n
ii ${Dir}/tract_space_coords_for_fdt_matrix4 -surface-seeds
${Dir}/SeedSpaceMetric.func.gii ${Dir}/fdt_matrix4.trajTEMP.wbsparse
$Caret7_Command -convert-matrix4-to-matrix2
${Dir}/fdt_matrix4.trajTEMP.wbsparse ${Dir}/fdt_matrix2.dconn.nii
The latest version of workbench has visualization for all of these file
types, and the next workbench tutorial should cover them.
Peace,
Matt.
On 4/15/14, 5:42 AM, "Sarah Parisot" <[email protected]> wrote:
>Hi Matt,
>
>Here is my probtrack call. I ran it for the left hemisphere.
>
>probtrackx2 --samples=merged
>--mask=/T1w/L_Cerebral_Trajectory_1.25.nii.gz
>--seed=100307.L.white.32k_fs_LR.surf.gii
>--waypoints=100307.L.white.32k_fs_LR.surf.gii
>--stop=100307.L.pial.32k_fs_LR.surf.gii
>--target4=L_Cerebral_Trajectory_1.25.nii.gz
>--seedref=L_Cerebral_Trajectory_1.25.nii.gz
>--dir=/data/probtrack100307/left --nsamples=5000 --cthr=0.2
>--steplength=0.3 --forcedir --meshspace=caret --nsteps=2000
>--fibthresh=0.05 --loopcheck --randfib=2 --forcefirststep --opd
>--omatrix1 --omatrix4 --sampvox=1.25 --verbose=1
>
>Thanks,
>Sarah
>
>On 14/04/14 19:05, Glasser, Matthew wrote:
>> Can you send us your probtrackx call?
>>
>> Peace,
>>
>> Matt.
>>
>> On 4/14/14, 1:01 PM, "Sarah Parisot" <[email protected]> wrote:
>>
>>> Dear all,
>>>
>>> I am working on brain parcellation based on structural connectivity
>>> matrices. I ran FSL's probtrackx on an HCP subject, seeding from the
>>> WM/GM 32k surface to get the seedxseed connectivity matrix (matrix1)
>>>and
>>> I am struggling a little with the outputs of probtrackx and the use of
>>> the workbench for visualization. It would be great if I could have some
>>> answers to a few questions:
>>>
>>> -I obtained a matrix1.dot file that I would like to be able to
>>>visualize
>>> using the connectome workbench. I tried running the
>>> probtrackx-dot-convert command (I used a metric file with all ones for
>>> all nodes as -row/col-surface.) but the converted file appears to be
>>>all
>>> zeros when I load it in the workbench. Maybe I'm using the wrong metric
>>> file?
>>>
>>> -Is there a way to keep knowledge of the different tracts evaluated
>>>from
>>> one seed point to another?
>>> I am getting an image that counts all the tracts that go through a
>>> voxel, but I would like to know how seed A is connected to seed B. I
>>>was
>>> told this information is kept in the 'matrix4' output, which apparently
>>> cannot be read at the moment.
>>>
>>> Thanks.
>>> Best Regards,
>>> Sarah
>>> _______________________________________________
>>> HCP-Users mailing list
>>> [email protected]
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>>
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