Creating Cortical Surfaces

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All of the steps below are contained in the scripts file /Volumes/data9/surface/scripts/@recon

To run this command type,

 /Volumes/data9/surfaces/scripts/@recon ec subjname

Where ec is the two-letter experiment code and subjname is the subject's name in the format lastname_firstname. The scripts assumes that all of the steps performed the script file @prep_dir have been performed (see Preparation for Creating Cortical Surface Models page) e.g.

 /Volumes/data9/surfaces/scripts/@recon BD doe_jane

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

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

Using FreeSurfer on the MacPro To Speed Up Surface Creation

To remotely login on the Mac Pro use ssh:

ssh –l username

To setup your account run the following commands:

chsh –s /bin/tcsh
echo 'set path = ( $path  /sw/bin /Applications/afni/afni_src/macosx_10.4_Intel)' >> ~/.cshrc
echo ‘setenv FREESURFER_HOME /Applications/freesurfer‘ >> ~/.cshrc
echo ‘source $FREESURFER_HOME/SetUpFreeSurfer.csh' >> ~/.cshrc
echo ‘mkdir ~/mount/data9‘ >> ~/.cshrc
echo ‘mount_afp -i afp://username@ ~/mount/data9‘ >> ~/.cshrc

Using the MacPro causes some permissions issues. The easiest way to fix this is to run as a super user each time you login:

sudo -s

Remember to change the default shell for the super user:

chsh –s /bin/tcsh

Now you should be able to edit any file like you would do from the iMac. To enable window forwarding so that you can open GUIs like afni remotely you’ll need to take the following steps:

  • Find your IP address using ifconfig. The address will be listed under the device en0, next to inet. For example in the following output the IP address is 129.106.326.192:
       inet6 fe80::216:cbff:fe84:414a%en0 prefixlen 64 scopeid 0x4 
       inet netmask 0xffffff00 broadcast
       ether 00:16:cb:84:41:4a 
       media: autoselect (1000baseT <full-duplex,flow-control>) status: active
  • Allow your computer to accept window forwarding from the PowerMac:
xhost +

  • From the window that is logged onto the PowerMac set the display IP address:

To exit enter exit twice (once to exit from being a super user and another time to exit from the remote login.

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