Hi,
two issue, please.
1- I understand how performed probtrackx with one FS cortical label, but if I have four FS cortical targets, Can I run them together?
When I trying to run
cd $SUBJECTS_DIR/Control02/surf
mris_convert rh.white rh.white.gii
mris_convert lh.white lh.white.gii
echo $SUBJECTS_DIR/Control02/label/rh.frontal.label > rh.area1.txt
label2surf -s rh.white.gii -o rh.frontal.gii -l rh.area1.txt
echo $SUBJECTS_DIR/Control02/label/rh.parietal.label > rh.area2.txt
label2surf -s rh.white.gii -o rh.parietal.gii -l rh.area2.txt
echo $SUBJECTS_DIR/Control02/label/rh.occipital.label > area3.txt
label2surf -s rh.white.gii -o rh.occipital.gii -l rh.area3.txt
echo $SUBJECTS_DIR/Control02/label/rh.temporal.label > area4.txt
label2surf -s rh.white.gii -o rh.temporal.gii -l rh.area4.txt
cd $SUBJECTS_DIR/Control02/surf
echo $SUBJECTS_DIR/Control02/surf/rh.frontal.gii $SUBJECTS_DIR/Control02/surf/rh.parietal.gii$SUBJECTS_DIR/Control02/surf/rh.occipital.gii $SUBJECTS_DIR/Control02/surf/rh.temporal.gii > $SUBJECTS_DIR/Control02/mri/targets.txt
cd $SUBJECTS_DIR/Control02/
/usr/local/fsl/bin/probtrackx2 -x $SUBJECTS_DIR/Control02/mri/Right_Thalamus.nii.gz -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --xfm=freesurfer2fa.mat --invxfm=fa2freesurfer.mat --forcedir --opd -s $SUBJECTS_DIR/Control02/DTI.bedpostX/merged -m $SUBJECTS_DIR/Control02/DTI.bedpostX/nodif_brain_mask --dir=$SUBJECTS_DIR/Control02/HS_prova --targetmasks=$SUBJECTS_DIR/Control02/surf/targets.txt --os2t
but the final output are still the same.
2- In freeview I visualize .labels and T1 in the correct orientation.
In FSL, the S/I/A/P labels are all correct (I can never tell with R/L), but orientation of T1 no. I know that orientation, as coded in the NIFTI, is a completely separate issue from how a given viewing tool chooses to display the data. Therefore, I suppose that FSL is respecting the orientation info. For visualization purpose, I should rotate T1 with fslswapdim, but how can I rotate probtrackx output?
Thanks,
S.
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