Dear FSL Community
I am having issues with using probtrackx2 and find_the_biggest. I have defined the subcortical seed ROI and the cortical target ROIs in diffusion space. I have double-checked the registration and all ROIs appear to be accurate when overlaid with the nodif image from the diffusion dataset. However, after running probtrackx2 and find_the_biggest, the seed mask has clearly moved from what was input into probtrackx2 so the output segmented ROI is no longer in the same space as the original input seed ROI. I have included the calls below:
probtrackx2 -x $USER/346137/seg/r_seed.nii.gz -l --onewaycondition --pd -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --forcedir --opd -s $USER/346137/diffusion.bedpostX/merged -m $USER/346137/diffusion.bedpostX/nodif_brain_mask --dir=$USER/346137/r_seg_output --targetmasks=$USER/346137/seg/r_targets.txt --os2t
find_the_biggest $USER/346137/r_seg_output/seeds_to_* $USER/346137/r_seg_output/r_segment
Thank you in advance!
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