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"), follow the additional steps here - and resume with step 5 on this page...

*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

• NOTE: The method I've show below divides the parcellation, orthogonally along its long axis.
  • There is also a method of using mris_divide_parcellation that specifies a unit of area for each seed.

echo "isthmuscingulate 3" > seed.isthmuscingulate.3.txt

• mris_divide_parcellation $recondir $hemi aparc.annot $txt ${hemi}.${splitN}split

*STEP 4: Use fcseed-config to record the parameters you wish to pass to your connectivity analysis.

Sample command: fcseed-config -segid 1010 -fcname mean.L_Posteriorcingulate.dat -fsd bold -mean -cfg mean.L_Posteriorcingulate.config

This example will use the FreeSurfer cortical segmentation for the left posterior cingulate (segID: 1010). For seed regions, we recommend generating the mean signal timecourse by using "-mean"

Now resume with step 5 on this page...