= FreeSurfer at the CBU = 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]] '''Automating conversion of the high resolution anatomical images extracted by freeSurfer (.mgz format) to a nifti format usable for spm coregistration:''' [[http://imaging.mrc.cbu.cam.ac.uk/imaging/FreesurferGoodies/convertToNifti|convertToNifti]] '''Copying the spm statistical maps used for coregistration from folder to folder (in matlab):''' [[http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferGoodies/copyFiles|copyFiles]] '''Coregister the freeSurfer and SPM high resolution anatomicals:''' [[http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferGoodies/coregisterSPMtoFreeSurfer|coregisterSPMtoFreeSurfer]] '''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]] '''Once you have all the labels you can bring it to SPM space:''' [[http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferGoodies/transformRAStoNative|transformRAStoNative]] '''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.