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

This page will outline how to split a full FreeSurfer aparc ROI 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

 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.

*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.
Sample commands:

 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.

 mris_divide_parcellation <recondir> <hemi> aparc.annot seed.isthmuscingulate.3.txt  ${hemi}.${splitN}split



*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.

Sample command:
          mri_annotation2label --subject <recondir> \
                               --hemi <hemi> 
                               --labelbase <hemi>.isthmuscingulate.3 
                               --annotation 3split 
                               --surface pial

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 | grep <hemi>.isthmuscingulate.3 |  sort -nr | sed -n ${splitN2},500p`

       (The above command lists all files in the label dir, greps for our label name,
        sorts numerically in reverse, then grabs all labels after the first 3)

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.

Sample command:

   mri_label2vol  --label <label>  --temp $SUBJECTS_DIR/<recondir>/mri/brainmask.nii.gz  --proj frac 0 1 .1  --subject <recondir> --hemi <hemi>  --regheader $SUBJECTS_DIR/<recondir>/mri/brainmask.nii.gz  --o <outsegname>

*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:

  set type    = mean                       # For seed regions, we recommend generating the  mean signal timecourse by using  "-mean"
  set segname = <hemi>.isthmuscingulate.split3.1

  fcseed-sess  -s <subject>    -segid 1 -o ${type}.${segname}.dat -seg <outsegname>  -fsd bold  -${type}  -cfg {type}.${segname}.config


Now resume with [[FsFastFunctionalConnectivityWalkthrough |step 5 on this page...]]