Dear All,

I want to use cingulate bundle as ROIs more exactly mask for fiber tracking.

Can someone explain please how I can use the 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 subjects?

Do I need to draw ROIs and how I can do this more accurate?

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