Note: this is a companion page to the FsFastFunctionalConnectivityWalkthrough page.

This page will outline how to split a full FreeSurfer aparc annotation into multiple seeds to use a portion of the full Freesurfer parcellation ("split parcellation") as your seed region.

*STEP 1: create a text file with the name of the full parcellation of interest and the number of seeds. Possible structures can be found here: $FREESURFER_HOME/average/colortable_desikan_killiany.txt

*STEP 2: use mris_divide_parcellation. This command will generate a new parcellation including your split ROI, as well as all original parcellations outside your chosen region.

set splitN = 3 <-this is the number of divisions to make echo "isthmuscingulate 3" > seed.isthmuscingulate.3.txt set splitstem = <hemi>.isthmuscingulate.3.split <-name for divided surface annotation

*STEP 3: use mri_annotation2label to create labels from the new annotation. This will create a label for each parcellation (including labels for regions outside of your desired seed region). The labels will be deposited in the subject's recondir/label directory.

To remove the excess labels, I've used this method:

@ splitN2 = $splitN + 1 <-this number will be helpful when removing excess labels

set rmextra = `find $SUBJECTS_DIR/<recondir>/label -maxdepth 1 -type f | \

echo " REMOVING excess labels " rm -v $rmextra set lbls = find $ldir -maxdepth 1 -type f | grep <hemi>.isthmuscingulate.3 | sort -nr <-grabs our seed labels

*STEP 4: check that you've grabbed the correct seed labels by loading them in tksurfer

*STEP 5: Use mri_label2vol on each of the split seed labels to obtain a segmentation volume for each.

*STEP 6: Use fcseed-config to record the parameters you wish to pass to your connectivity analysis.

Sample command for running the mean time course and using the first (1) of the 3 seed split:

Now resume with step 5 on this page...