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Mapping automatic segmentations to the functional space

1.0 Mapping the segmentations

The cortical and subcortical segmentations automatically generated by freesurfer can be mapped into the functional space, which can be useful for doing region of interest (ROI) analysis. This can be done with aseg2feat:

aseg2feat --feat fbert.feat --aseg aparc+aseg

and This command will create fbert.feat/reg/freesurfer/aparc+aseg.nii.gz. These are segmentations, meaning that each voxel has an integer value that corresponds to a particular structure. The mapping from structure number to name is given in ${FREESURFER_HOME}/FreeSurferColorLUT.txt.

2.0 Creating binary masks

The segmentation for a particular structure can be extracted to create a binary mask (i.e., a volume where the voxel value is 1 if it is in the structure and 0 otherwise). To make a binary mask of the left putamen, which has been assigned label 12 (see ${FREESURFER_HOME}/FreeSurferColorLUT.txt), use the following command:

avwmaths ./fbert.feat/reg/freesurfer/aparc+aseg.nii.gz \
    -thr 12 -uthr 12 \
    ./fbert.feat/reg/freesurfer/lh.putamen.nii.gz

To view this binary mask on the anatomical:

tkmedit bert orig.mgz -aux brain.mgz \
    -overlay ./fbert.feat/reg/freesurfer/lh.putamen.nii.gz \
    -overlay-reg ./fbert.feat/reg/freesurfer/anat2exf.register.dat \
    -fthresh 0.5 -fmid 1 -fslope 1 \
    -segmentation ${SUBJECTS_DIR}/bert/mri/aparc+aseg.mgz \
    ${FREESURFER_HOME}/FreeSurferColorLUT.txt

You should see the image below:BR attachment:tkm-lh.putamen-cor-128-small.jpg