= 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):'''
{{{
#!/bin/sh
#
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.