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