Hi Jane,
it seems to me that you have not specified the seed space (i.e., using --seedref) and you should remove the space after the equal sign in: "--xfm= xfms/standard2diff.mat”.
If you define a single mask volume containing two bilateral ROIs, you will get the number of streamlines from *both* of them to all the other seed masks that you have specified. If that’s not what you want, you should put each ROI in a separate volume.
As a suggestion, try to use nonlinear registration (e.g., with FNIRT) when registering your subject’s MPRAGE to the MNI template.
Hope this helps, cheers,
Matteo
> On 15 Dec 2017, at 03:20, Jane K <[log in to unmask]> wrote:
>
> Hi all,
>
> I am new to analyzing DTI data, so I would really appreciate some help with this! This is what I have done so far:
>
> topup correction --> bet extraction of brain --> eddy correction --> dtifit to get the vector fields --> bedpostx
>
> Then I used flirt to find the transformation matrices between DTI scans, MPRAGE structural scans and MNI standard brain (avg152T1_brain.nii.gz that comes with FSL package). I also created two anatomical ROI masks with FSLView, in the same space as the MNI standard brain, and put the file paths in masks.txt.
>
> Then I ran probtrackx using the following script under each subject's .bedpostx directory
>
> probtrackx2 --network -x masks.txt -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --xfm= xfms/standard2diff.mat --forcedir --opd -s merged -m nodif_brain_mask --dir= outputdirectory
>
> The problem is in the end if I check waytotal it always says 0 0. One of the masks I'm using is a bilateral ROI mask, could that be the reason?
>
> Thanks in advance!!
>
> Best,
> Jane
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