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| See here for the general '''[http://surfer.nmr.mgh.harvard.edu/ Freesurfer home page]''' and '''[http://surfer.nmr.mgh.harvard.edu/fswiki FreeSurfer Wiki]'''. | See here for the general '''[[http://surfer.nmr.mgh.harvard.edu/|Freesurfer home page]]''' and '''[[http://surfer.nmr.mgh.harvard.edu/fswiki|FreeSurfer Wiki]]'''. |
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| 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]'''. | 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]]'''. |
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| [http://ltl.tkk.fi/wiki/images/1/18/Henriksson_fMRI09_visuquan.pdf An introduction tutorial to freesurfer by our own Linda Henriksson] | [[http://ltl.tkk.fi/wiki/images/1/18/Henriksson_fMRI09_visuquan.pdf|An introduction tutorial to freesurfer by our own Linda Henriksson]] |
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| [http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferGoodies/generatefreesurferscripts A matlab function for semi-automated batch recon-all] | [[http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferGoodies/generatefreesurferscripts|A matlab function for semi-automated batch recon-all]] |
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| [http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferGoodies/AutomaticLabeling AutomaticLabeling] | [[http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferGoodies/AutomaticLabeling|AutomaticLabeling]] |
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| [http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferGoodies/batchcreateRegistrationFiles batchcreateRegistrationFiles] | [[http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferGoodies/batchcreateRegistrationFiles|batchcreateRegistrationFiles]] |
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| [http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferGoodies/transformRAStoNative transformRAStoNative] | [[http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferGoodies/transformRAStoNative|transformRAStoNative]] |
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| [http://openwetware.org/wiki/Beauchamp:FreeSurfer#Creating_Flat_Maps Creating Flat Maps] | [[http://openwetware.org/wiki/Beauchamp:FreeSurfer#Creating_Flat_Maps|Creating Flat Maps]] |
FreeSurfer at the CBSU
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:
Creating the register.dat and the v2r.dat that are needed for the transformation from freeSurfer RAS space to your subject native space
Once you have all the labels you can bring it to SPM space:
A useful tutorial by Michael S. Beauchamp on how to create flat maps
Let me know if you encounter any problems using this code.