Hi there,
I have a question regarding probtrackX. We acquired several scans of the same participants using the same sequence, 2 in one session on one day with repositioning, and 2 on another also with repositioning. I convered the DICOM into niftii with MRIconvert, then I ran bedpost / probtrackX (linear registration, see command below) on all of them using a unilateral BA4 seed mask obtained from the wfu_pickatlas and the medulla termination/waypoint mask plus a midline exclusion mask. I then thresholded the resulting fdt_paths at 50 using fslmaths and then extracted the mean FA of the resulting corticospinal tract (see command below). Unexpectedly, I get very different values using this technique and was wondering whether I did something wrong.
Example of one participant:
Day1:
FA voxels volume
0.444591 461 3688
0.429658 2166 17328
Day2:
0.399608 2970 23760
0.404466 3113 24904
Thanks very much for your help.
Cheers,
Torsten
ProbtrackX command:
for i in $Bedpost_Dirs_1; do
/usr/local/FSL/fsl-4.1.5-centos4_64/bin/probtrackx --mode=seedmask -x /home/tr83/MY_ANALYSIS/Tracts/BA4l_dil2.hdr -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --xfm=$i/std2S0.mat --avoid=/home/tr83/MY_ANALYSIS/Tracts/midline_mask.nii --stop=/home/tr83/MY_ANALYSIS/Tracts/Medulla_dil2.hdr --forcedir --opd -s $i/merged -m $i/nodif_brain_mask --dir=$i/BA4l_2_Medulla_waypoint_termination --waypoints=/home/t/tr/tr83/MY_ANALYSIS/Tracts/medulla_dil2_waypoint.txt
done
FSL stats command to extract values:
for i in $DTI_Dirs; do
cd $i
fslmaths $i.bedpostX/BA4l_2_Medulla_waypoint_termination/fdt_paths.nii.gz -thr 50 -bin $i.bedpostX/BA4l_2_Medulla_waypoint_termination/fdt_paths_50;
fslstats dti_FA_2_std.nii.gz -k $i.bedpostX/BA4l_2_Medulla_waypoint_termination/fdt_paths_50.nii.gz -M -V;
done
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