Transform from fsaverage to fsnative

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1

Hi,

Hopefully a relatively straightforward question.

How do I transform an atlas in fsaverage space into a subjects fsnative space?

I am using fmriprep and imagine the necessary transforms are somewhere in the freesurfer/subject/mri/transforms folder but it isn’t clear to me.

Thanks!

Rob

2

You’ll want the SUBJECTS_DIR environment variable to point to the directory with your reconstructed subjects in it. Then you can just use mri_surf2surf.

mri_surf2surf --srcsubject fsaverage --trgsubject $SUBJECT --hemi $HEMI \
    --sval $INPUT --tval $OUTPUT
3

what are the values for $INPUT and $OUTPUT. I have a similar problem, I have the surface values for subject in fsaverage surface and would like to transform it back to native surface for the subject.

4

$INPUT is the file you want to transform, $OUTPUT is what you want the transformed file to be called.

5

Thanks, so the $INPUT can be for example surface activation for a subject in fsaverage surface, and output the activation on subject native surface?

6

Yes, that’s exactly right.

7

oh awesome! just following up on, next I want to move the activation from subject surface onto subject volume, and using a mri_surf2vol :
mri_surf2vol --o $OUTPUT_FILE --subject $SUB_ID --so $SUBJECTS_DIR/$SUB_ID/surf/lh.inflated $SUBJECTS_DIR/$SUB/sub_activation_on_native_surface.nii

however I am getting an error saying there is no match. what could be going on?

8

Hard to tell without the error text. And could you explain the goal of moving activation into the volume space? I ask for two reasons:

  1. If you project the data onto the voxels intersecting the pial surface, you’ll get different data than projecting onto the gray/white boundary, or the mid-thickness surface. Your choice of parameters is going to depend on what you’re trying to do, so I can’t make a suggestion for a better command.
  2. I can’t think of a good reason to project activation maps from the surface to the volume. The main reason I would use mri_surf2vol is to project morphometric data, parcellations, or surface indices into the volume space, so that I can use them to create ROIs in the original voxel space.