How to get ROIs from Kastner FreeSurfer Atlas

Published by Gizem on

How to get ROIs from Kastner FreeSurfer Atlas?

Left hemisphere

./surf2vol.sh ./Kastner2015Labels-LH.mgz E01S05 lh freesurfer $SUBJECTS_DIR/E01S05/mri/lh.kastner_freesurfer.mgz

Right hemisphere

./surf2vol.sh ./Kastner2015Labels-LH.mgz E01S05 rh freesurfer $SUBJECTS_DIR/E01S05/mri/rh.kastner_freesurfer.mgz

Left hemisphere

mri_surf2surf --srcsubject fsaverage --sval /Users/X/Data/freesurfer_v53/freesurfer/Kastner2015Atlas/perc_VTPM_surf_all_lh.gii.mgz --trgsubject E01S05 --tval $SUBJECTS_DIR/E01S05/mri/lh_kastner_surf.nii --hemi lh 

Right hemisphere

mri_surf2surf --srcsubject fsaverage --sval /Users/X/Data/freesurfer_v53/freesurfer/Kastner2015Atlas/perc_VTPM_surf_all_rh.gii.mgz --trgsubject E01S05 --tval $SUBJECTS_DIR/E01S05/mri/rh_kastner_surf.nii --hemi rh
Left hemisphere
tksurfer E01S05 lh  inflated -overlay $SUBJECTS_DIR/E01S05/mri/lh_kastner_surf.nii
Right hemisphere
tksurfer E01S05 rh  inflated -overlay $SUBJECTS_DIR/E01S05/mri/rh_kastner_surf.nii
  • Choose the relevant frame for the area of interest (see in ROIfiles_Labeling.txt)
  • Apply a reasonable threshold (for me >=30%)
  1. Click around the area liberally
  2. Click on ‘Make closed path’ on the interface
  3. Click on the area
  4. Choose ‘Custom fill’ tool and fill with the settings shown below
 
 
  • Then convert this label to volume with ‘mri_label2vol’
Left Hemisphere
mri_label2vol --label /Users/X/Data/Experiments_fMRI/01_IMD/fsAnatomical/E01S07/label/lh_e01s07_Kastner_LO2.label --temp /Users/X/Data/Experiments_fMRI/01_IMD/res/meanfuncs/meanuafe01s07_IMD_24052016-0003-00009-000009-01.nii --reg /Users/X/Data/Experiments_fMRI/01_IMD/fsAnatomical/E01S07/stats/register.dat --fillthresh 0 --proj frac 0 1 .5 --subject E01S07 --hemi lh --o /Users/X/Data/Experiments_fMRI/01_IMD/fsAnatomical/Kastner_ROIs/lh_E01S07_Kastner_LO2.nii  
Right Hemisphere 
mri_label2vol --label /Users/X/Data/Experiments_fMRI/01_IMD/fsAnatomical/E01S07/label/rh_e01s07_Kastner_LO2.label --temp /Users/X/Data/Experiments_fMRI/01_IMD/res/meanfuncs/meanuafe01s07_IMD_24052016-0003-00009-000009-01.nii --reg /Users/X/Data/Experiments_fMRI/01_IMD/fsAnatomical/E01S07/stats/register.dat --fillthresh 0 --proj frac 0 1 .5 --subject E01S07 --hemi rh --o /Users/X/Data/Experiments_fMRI/01_IMD/fsAnatomical/Kastner_ROIs/rh_E01S07_Kastner_LO2.nii