How to get ROIs from Kastner FreeSurfer Atlas?

Surface based → Volume based

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%)
  • Click around the area liberallyClick on ‘Make closed path’ on the interface
  • Click on the area
  • 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