Anatomical ROI analysis
This tutorial gives a brief introduction to anatomical ROI analysis which includes working with label files, extracting ROI measures from the anatomical data, group statistics etc. Make sure you have set you SUBJECTS_DIR to correct location.
Relationship between segmentation, parcellation, and LookUp Table (LUT)
Open your subjectID in tkmedit using the following command
tkmedit <subjectID> orig.mgz -aux aparc+aseg.mgz \ -seg aparc+aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt
Open another terminal to load the subject in tksurfer, using the following command.
tksurfer <subjectID> lh inflated -annot aparc.annot
Run the following command to display the contents of LUT
less $FREESURFER_HOME/FreeSurferColorLUT.txt
Click on a point on the image loaded in tkmedit. You can see the structure name in the tkmedit toolbar. Look at the Aux value, find value in LUT, which you have opened using the command mentioned above. See that it is the same structure as listedin tkmedit.
Click on a point in tksurfer and see structure name. Note that the name does not have lh or rh in it. Click on the Save Point tool button, and then click on Goto Point tool button in tkmedit. You will notice that the structure name in tkmedit has lh or rh in it.
Label files
This section gives the details of commands to load an existing label file in text editor, tkmedit, and tksurfer.
To load an existing label, for example lh.cortex.label, run
less <subjectID>/label/lh.cortex.label
To load a label in tkmedit, first load the subject you want to work on, in tkmedit.
tkmedit <subjectID> orig.mgz
Then on the tkmedit toolbar, go to File-> Label --> load label --> lh.cortex.label
To load the label in tksurfer, make sure you load the subject in tksurfer.
tksurfer subject lh inflated
On the tksurfer toolbar, go to File --> label --> LoadLabel --> lh.cortex.label You can also load the label from the tksurfer tool bar using Ctrl - right mouse button on the 'Show labels' tool button. Browse the label you want to load and click 'OK'