Diff for "FreesurferGoodies" - MRC CBU Imaging Wiki
location: Diff for "FreesurferGoodies"
Differences between revisions 15 and 16
Revision 15 as of 2012-03-07 16:58:56
Size: 2130
Editor: YaaraErez
Comment:
Revision 16 as of 2012-03-07 17:05:08
Size: 2302
Editor: YaaraErez
Comment:
Deletions are marked like this. Additions are marked like this.
Line 1: Line 1:
= FreeSurfer at the CBSU =
Line 2: Line 3:
'''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]'''.
Line 4: Line 5:
[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]'''.
Line 6: Line 7:
'''Here are some freesurfer goodies that you might find useful:''' Here are some freesurfer goodies that you might find useful:'''
Line 21: Line 22:
first load the study average inflated cortical surface using tksurfer:  * First load the study average inflated cortical surface using tksurfer:
Line 26: Line 27:
Make sure you have no selected vertices.  * Make sure you have no selected vertices.
Line 28: Line 29:
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.
Line 30: Line 31:
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.
Line 32: Line 33:
'''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]

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]

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.

CbuImaging: FreesurferGoodies (last edited 2023-10-02 20:20:42 by DaceApsvalka)