Convert volume GLM to surface with fMRIprep output

1

Hi,

I am trying to put my FSL GLM results onto the fsaverage surface for:

  1. draw group ROI with my functional localizer
  2. do surface-based searchlight with CosmoMVPA

I have done fMRIprep on my dataset, and get:
anat/_from-T1w_to-fsnative_mode-image_xfm.txt

Could anybody help me with the next step?

I checked a thread here:
Volume to surface mapping (mri_vol2surf) using fmriprep outputs?

and tried:

lta_convert --initk sub-1_from-T1w_to-fsnative_mode-image_xfm.txt --outlta sub-1_from-T1w_to-fsnative_mode-image_xfm.lta --outreg sub-1_from-T1w_to-fsnative_mode-image_xfm.dat --src …/…/…/fsl/data_listening_MNI_orig/sub-1.nii.gz --trg …/…/…/freesurfer/sub-1/mri/T1.mgz --subject sub-1

It returned:

7.1.0

–initk: sub-1_from-T1w_to-fsnative_mode-image_xfm.txt input ITK txt transform.
–outlta: sub-1_from-T1w_to-fsnative_mode-image_xfm.lta output LTA.
–outreg: sub-1_from-T1w_to-fsnative_mode-image_xfm.dat output reg.dat matrix.
–src: …/…/…/fsl/data_listening_MNI_orig/sub-1.nii.gz src image (geometry).
–trg: …/…/…/freesurfer/sub-1/mri/T1.mgz trg image (geometry).
–s: sub-1 subject name
Transform: AffineTransform_float_3_3
ERROR readITK: Transform type unknown!

Not sure what that even means…

Thanks!

1 Like
2

I don’t know about those error messages, but as a general practice if you want to do surface analyses, I suggest you make the surfaces as early in the pipeline as possible, and keep the dataset as surfaces all the way through analysis, rather than trying to convert volumetric analysis results to surfaces. fMRIPrep can generate fsaverage preprocessed images, so that shouldn’t be an issue here.

More of my thinking behind the preprocess-to-surfaces-and-keep-as-surfaces advice is at https://mvpa.blogspot.com/2020/01/working-with-surfaces-musings-and.html.

1 Like
3

Thank you very much for your suggestion! I will look into it.

I really like your blog!