Dear All,
I want to use cingulate bundle as ROIs more exactly mask for fiber tracking.
Can I use different aseg than the one from Freesurfer for examples can I use segmentation from JHU-WhiteMatter-labels-1mm.nii.gz and their labels JHU-WhiteMatter-labels-1mm.txt to get a mask of my cingulate bundle in my diffusion space for each individual subject.
Is the following correct:
1) mri_convert -rl [path to subject]/DATA/s001/nodif.nii.gz -rt nearest JHU-WhiteMatter-labels-1mm.nii.gz s001_aseg2dif.nii.gz
2) fslmaths /[path to subject]/DATA/s001_aseg2dif.nii.gz -uthr 35 -thr 35 /[path to working directory]/ROIS/Cingulum_(cingulate_gyrus)_R.nii.gz
3) fslmaths Cingulum_(cingulate_gyrus)_R.nii.gz –div 35 Cingulum_(cingulate_gyrus)_R.nii.gz
If I want to run for the cingulate bundle the tractography should I repeat this steps for:
36 Cingulum_(cingulate_gyrus)_L 37 Cingulum_(hippocampus)_R 38 Cingulum_(hippocampus)_L
Thank you for your help. Antonella