FreesurferGoodies - MRC CBU Imaging Wiki

Revision 16 as of 2012-03-07 17:05:08

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FreeSurfer at the CBSU

See here for the general [http://surfer.nmr.mgh.harvard.edu/ Freesurfer home page] and [http://surfer.nmr.mgh.harvard.edu/fswiki FreeSurfer Wiki].

Refer to this page if you need to set up your [http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferInformation Freesurfer environment here at the CBSU].

Here are some freesurfer goodies that you might find useful:

[http://ltl.tkk.fi/wiki/images/1/18/Henriksson_fMRI09_visuquan.pdf An introduction tutorial to freesurfer by our own Linda Henriksson]

[http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferGoodies/generatefreesurferscripts A matlab function for semi-automated batch recon-all]

Compute the study average cortical surface (the average cortical surface across the subjects in your study): 

#
make_average_subject --subjects   Subject1 Subject2 Subject3 --out myAverage

Draw your own ROIs (labels) on the study average inflated cortical surface:

  • First load the study average inflated cortical surface using tksurfer: 

tksurfer myAverage lh inflated -curv
  • Make sure you have no selected vertices.
  • Then make a series of left clicks on the surface to outline the label you want to draw. Then click the "Make Closed Path" button.

  • Click on the Custom fill button, this will bring up a dialog box with several fill options. Click the one that says "Up to and including boundaries" and then click the fill button. This should create a label which you can now save with labels -> save as.

Automatic labeling of your individual subjects from the ROI you have just drawn on the study average cortical surface:

[http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferGoodies/AutomaticLabeling AutomaticLabeling]

Creating the register.dat and the v2r.dat that are needed for the transformation from freeSurfer RAS space to your subject native space

[http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferGoodies/batchcreateRegistrationFiles batchcreateRegistrationFiles]

A useful tutorial by Michael S. Beauchamp on how to create flat maps

[http://openwetware.org/wiki/Beauchamp:FreeSurfer#Creating_Flat_Maps Creating Flat Maps]

Let me know if you encounter any problems using this code.