FreesurferGoodies - MRC CBU Imaging Wiki

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FreeSurfer at the CBU

See here for the general Freesurfer home page and FreeSurfer Wiki.

Refer to this page if you need to set up your Freesurfer environment here at the CBSU.

Here are some freesurfer goodies that you might find useful:

An introduction tutorial to freesurfer by our own Linda Henriksson

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:

AutomaticLabeling

Automating conversion of the high resolution anatomical images extracted by freeSurfer (.mgz format) to a nifti format usable for spm coregistration:

convertToNifti

Copying the spm statistical maps used for coregistration from folder to folder (in matlab):

copyFiles

Coregister the freeSurfer and SPM high resolution anatomicals:

coregisterSPMtoFreeSurfer

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

batchcreateRegistrationFiles

Once you have all the labels you can bring it to SPM space:

transformRAStoNative

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

Creating Flat Maps

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