How to map rois from freesurfer average surface to subject surface?

AFNI Message Board
1

Hi,

For example, map the “lh.V1_exvivo.label” file from freesurfer/fsaverage folder to subject surface. This file actually has been transformed to subject surface, localized in the freesurfer output subject/label folder, but @SUMA_Make_Spec_FS skipped this file. How to transform this file as others by @SUMA_Make_Spec_FS.

And for another example, label files provided by literatures, which are in fsaverage surface, but not provided by freesurfer, how to transform this kind of rois to subject surface?

Thank you,
2086

2

Greetings 2086,

Do you already have the labels in an AFNI related format (niml.dset or gii)? You can use SurfToSurf to go from one surface space to another (e.g. FS Average to subject or back again). You can also transform that fsaverage space label to the standard label (std.141.*) and then map it to any surface.

-Peter

3

Hi Peter,

Thanks for your reply. They are in freesurfer label file format. The head 10 lines of the label file:

#!ascii label , from subject vox2ras=TkReg
4727
86127 20.805 -72.558 8.916 0.800000
86130 4.070 -85.431 -20.955 0.900000
51746 7.490 -75.863 -26.479 0.600000
111576 19.541 -75.378 12.541 0.500000
21027 7.490 -75.863 -26.479 0.800000
111581 20.151 -74.139 8.433 0.900000
86125 20.805 -72.558 8.916 0.800000
38548 21.792 -72.258 8.772 0.800000

Do you know what to do with this format?

Thank you,
2086

4

Yes.

The first step is to convert the label into an annotation in Freesurfer using mris_label2annot[/url]. Once you have that, you can use [url=https://afni.nimh.nih.gov/pub/dist/doc/program_help/FSread_annot.html]FSread_annot[/url] to convert it to SUMA. You may need to also run [url=https://afni.nimh.nih.gov/pub/dist/doc/program_help/ROI2dataset.html]ROI2dataset[/url] depending on what you want to do. And then [url=https://afni.nimh.nih.gov/pub/dist/doc/program_help/SurfToSurf.html]SurfToSurf with padding should take it the final step.

-Peter

5

Hi Peter,

Thanks for your answer.

I found that @FSlabel2dset can transform freesurfer label file to SUMA dset directly.

And for the second example in the original question, that is the freesurfer label file in fsaverage surface need to transform to subject surface first, can be solved by this:

As the results of @FSlabel2dset is in subject original dense mesh, I want to ask a following question, how to transform the dset in subject original mesh to subject std.141 mesh?

Thank you,
2086

6

Assuming you’ve already run @SUMA_Make_Spec_FS along with the MapIcosahedron step, you can use SurfToSurf. There’s an example in the MapIcosahedron help file at the end.

7

Hi Peter,

Thank you very much!
ps: The “-output_params NearestNode” parameter is needed for the label/roi file derived NN_dset.

Best,
2086