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FreeSurfer Subcortical Segmentation

In subcortical segmentation, each voxel in the normalized brain volume is assigned one of about 40 labels, including:

FreeSurfer now automatically runs automated labeling of the brain volume and this is included in all versions of the September 2005 release. However, if you processed your anatomical data using previous versions and you wish to obtain the automated labels, you can just run the subcortical segmentation separately. It is important to note that the September 2005 release of FreeSurfer by default uses the automatically segmented brain volume (ASEG) to segment the white matter volume (WM). You must therefore use the -noedit_wm_with_aseg flag to ensure that it preserves and uses the white matter volume (WM) edits that you made, IF you rerun any later steps on your previously edited data -- e.g. if for some reason you wish to regenerate final surfaces.

So, to obtain automatically segmented volumes for the first time, run:

recon-all -subcortseg -segstats -subjid <subject name>

The process flowchart below shows the various input and output files created along the way.

Process Flow

recon-all step

Input

Command Line

Output

["recon-all"] -autorecon1 -subjid subj

orig/001.mgz

["mri_motion_correct2"] -i orig/001.mgz -i orig/002.mgz -o rawavg.mgz

rawavg.mgz

orig/002.mgz

rawavg.mgz

["mri_convert"] rawavg.mgz orig.mgz --conform

orig.mgz

orig.mgz

["mri_convert"] orig.mgz orig.mnc

orig.mnc

orig.mnc

(4 iterations of) ["nu_correct"] -clobber nu0.mnc nu1.mnc

nu4.mnc

nu4.mnc

["mri_convert"] nu4.mnc nu.mgz

nu.mgz

nu.mgz

["talairach2"] subjid -mgz

transforms/talairach.xfm

nu.mgz

["mri_normalize"] nu.mgz T1.mgz

T1.mgz

T1.mgz

["mri_watershed"] T1.mgz brain.mgz

brain.mgz

Check skullstrip (brain.mgz), talairach (transforms/talairach.xfm), and normalization (brain.mgz or T1.mgz - mean wm voxel value = 110)

["recon-all"] -autorecon2 -no_edit_wm_with_aseg -keepwmedits -subjid subj

brain.mgz

["mri_em_register"] -mask brain.mgz -p .5 -fsamples fsamples.mgz nu.mgz $GCA transforms/talairach.lta

transforms/talairach.lta

nu.mgz

brain.mgz

["mri_ca_normalize"] -mask brain.mgz nu.mgz $GCA transforms/talairach.lta norm.mgz

norm.mgz

nu.mgz

transforms/talairach.lta

brain.mgz

["mri_ca_register"] -cross-sequence -mask brain.mgz -T transforms/talairach.lta norm.mgz $GCA transforms/talairach.m3z

transforms/talairach.m3z

transforms/talairach.lta

norm.mgz

norm.mgz

["mri_ca_label"] -cross-sequence norm.mgz transforms/talairach.m3z $GCA aseg.mgz

aseg.mgz

transforms/talairach.m3z

brain.mgz

["mri_normalize"] -mask brain.mgz nu.mgz T1.mgz

T1.mgz

nu.mgz

T1.mgz

["mri_mask"] T1.mgz brain.mgz brain.mgz

brain.mgz

brain.mgz

brain.mgz

["mri_segment"] brain.mgz wm.mgz

wm.mgz

wm.mgz

["mri_edit_wm_with_aseg"] wm.mgz aseg.mgz wm.mgz

wm.mgz

aseg.mgz

The automatic subcortical segmentation can take many hours to complete.

To view the segmentation, use this command:

tkmedit <subject name> norm.mgz -segmentation mri/aseg $FREESURFER_HOME/tkmeditColorsCMA