To FSL/Freesurfer experts, I have been trying for the last few weeks to perform whole-brain probabilistic tractography using FSL's probtrackx2. After solving a number of issues, I believe I am calling the command correctly, but it has already taken 5 days and wondering if I am going in the right direction.
Our data compromises of T1-weighted images with spatial resolution of 1x1x1 mm^3. I have called the following command on a 64GB RAM CPU system, using the native-freesurfer Desikan (68 ROI) parcellation. probtrackx2 -s ./merged -m ./nodif_brain_mask.nii -x ./rois.ascii --seedref=./rawavg.nii --xfm=./fs2dti.mat --targetmasks=./rois.ascii --dir=../probtrackresults/ --forcedir --s2tastext --omatrix1 What I would like to know if anyone has successfully performed whole-brain tractography with what certain specifications. For example, the number of parcellations you used, computer speed etc. How long did it take to run, and if it is not an issue, what is the command you used? I am obviously aware by reducing the number of vertices it can significantly decrease the running time, however I do not want to kill the running command. Thanks, Alistair Perry
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