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Creating the surface

To create the surface, run the script


This script should be run in the home directory of the experiment, e.g.

 cd /Volumes/data1/UT/DB

FreeSurfer will take about 6 - 8 hours to complete. After it is finished, run the @finish script, described on the following page:

  1. Final touches and using Cortical Surface Models

Be forewarned that use of this script on the iMacs will hamper system performance when the two hemispheres are simultaneously processed.

@recon assumes that all of the steps performed by the script file @prep_dir have been performed, see Preparation for Creating Cortical Surface Models


All of the steps below are contained in the scripts file; information about them is included here for educational purposes. For the old web page describing an earlier incarnation of @recon, please see OLD version of Creating Cortical Surface Models

Running FreeSurfer

The cortical surface reconstruction program recon-all has many options for processing the files, which are listed on the wiki: The easiest option is to run the entire file stream with the following command:

recon-all –all –s subjID

Often this will result in errors because FreeSurfer has permissions issues when copying and appending files. Processor usage can be checked using the program top in another window. If recon-all has been running one subprogram for an inordinate amount of time you can kill it using ctrl-c from the window where you are running recon-all. Reset the permissions so everyone can read and write files from the subject’s directory:

sudo chmod –R 777 $SUBJECTS_DIR/subjID

After resetting the permissions you should check where the program crashed by viewing recon-all-status.log in the subject’s scripts folder. Check the FreeSurfer wiki on how to restart the file stream from where the program crashed. For example, if the program during CA Normalize the program can be restarted using the following line:

recon-all –nogcareg –autorecon2 –autorecon3 –s subjID

Since the all the Macs in the lab are multiprocessor machines, the program can delegate each hemisphere to a single processor. To do this recon-all first needs to preprocess the anatomical data and then identify the white matter:

recon-all -autorecon1 -s subjID
recon-all -autorecon2 -s subjID -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nofinalsurfs -nosmooth2 -noinflate2 –nocortribbon

After the white matter has been defined, recon-all can process the two hemispheres separately using separate log and status files:

recon-all -s subjID -hemi lh -log $SUBJECTS_DIR/subjID/scripts/recon-all_lh.log -status $SUBJECTS_DIR/subjID/scripts/recon-all-status_lh.log -tessellate -smooth1 -inflate1 -qsphere -fix -finalsurfs -smooth2 -inflate2 -cortribbon -autorecon3 &; recon-all -s subjID -hemi rh -log $SUBJECTS_DIR/subjID/scripts/recon-all_rh.log -status $SUBJECTS_DIR/subjID/scripts/recon-all-status_rh.log -tessellate -smooth1 -inflate1 -qsphere -fix -finalsurfs -smooth2 -inflate2 -cortribbon -autorecon3

Alternatively you can use the script in the surfaces folder, which runs recon-all in the manner described above:

/surfaces/@recon-all_sep_hemi –subj subjID

Making a Pial Envelope

It can also be useful to have a pial "envelope" that holds the whole brain. For instance, electrodes can be mapped to this surface with the guarantee that they will be visible in any surface model and not buried in cortex. The command to make a pial envelope is

 set subjid = pasalar_siavash
 set SUBJECTS_DIR = /Volumes/data9/surfaces/{$subjid}/
 setenv SUBJECTS_DIR /Volumes/data9/surfaces/{$subjid}/
 set ec = SP
 recon-all -s $ec -localGI

This command requires that Matlab be in your path; you will receive an error if it is not. You may also not be able to run multiple copies of Matlab at once, so you should quit all open Matlabs before executing. This command also computes a local gyrification index, which may be decreased in diseases or disorders and could be interesting to look at.

Sample Subjects To Look At

Condensed Notes


When errors were encountered during autorecon-all


Pretty complete Notes


covers merging in afni, running recon-all, creating SS500, creating sulc.asc files, aligning to experimental data