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= FreeSurfer at the CBSU = | |
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'''Refer to this page if you need to set up your freesurfer environment here 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]'''. |
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[http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferInformation CBU FreesurferInformation] | 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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'''Here are some freesurfer goodies that you might find useful:''' | Here are some freesurfer goodies that you might find useful:''' |
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first load the study average inflated cortical surface using tksurfer: | * First load the study average inflated cortical surface using tksurfer: |
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Make sure you have no selected vertices. | * Make sure you have no selected vertices. |
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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. | * 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. |
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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. | * 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. |
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'''Automatic labeling of your individual subjects from the ROI you have just drawn on the study average cortical surface''' | '''Automatic labeling of your individual subjects from the ROI you have just drawn on the study average cortical surface:''' |
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] 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. [http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferGoodies/AutomaticLabeling AutomaticLabeling] [http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferGoodies/batchcreateRegistrationFiles batchcreateRegistrationFiles] [http://openwetware.org/wiki/Beauchamp:FreeSurfer#Creating_Flat_Maps Creating Flat Maps] Let me know if you encounter any problems using this code. #
make_average_subject --subjects Subject1 Subject2 Subject3 --out myAverage
Draw your own ROIs (labels) on the study average inflated cortical surface: tksurfer myAverage lh inflated -curv
Automatic labeling of your individual subjects from the ROI you have just drawn on the study average cortical surface: