Register preprocessed fMRI to freesurfer surface reconstruction

[pettitta]

Hi there,

I recently ran all of my subjects resting state scans through fmirprep and then through the functional processing pipeline in xcpEngine. The output of xcpEngine is a preprocessed 4d functional image (nii.gz) in T1w subject space. I have also processed every participant’s T1w anatomical image using reconall and have a surface reconstruction for each participant. Is there any way to register the processed 4d functional file to the surface reconstruction image? Additionally, if anyone has any resources for how to then do surface based ROI analyses using parcellations in surface space, that would be great! Let me know if anything I’ve asked was unclear and I’m happy to rephrase or expand on it.

Adam

[Ursula_Tooley]

I am doing something similar–I asked a friend and actually just ended up using bbregister between the functional reference image and the freesurfer anatomical, and then mri_vol2surf to get the processed functional data in surface space. I read the thread here but the transform fmriprep outputs didn’t look like it was suited perfectly for post-xcp data.

Here’s some threads on it:

Fmriprep: Which registration file is used for resampling BOLD to surface space?

Hi all, After preprocessing my data using fmriprep, I would like to run my voxel-wise BOLD regression in T1w volume space and then sample my results to fsnative surface space. Does anyone know which registration file fmriprep uses to sample the BOLD time series in original space to the fsnative surface space? And is there a transformation matrix in the fmriprep output which would give me those voxels used to create the BOLD time series in surface space later on so that I can limit the number of…

From volume to surface: registration file for mri_vol2surf

Hi, I am trying to bring the volumetric brain data (brought to the mni space) onto surface for visualization purposes. I came across with freesurfer’s “mri_vol2surf” tool, which is also embedded in nipype. This tool requires an input described as “registration file.” Does anyone have an idea, what it is exactly or how to generate it? Thanks in advance!

Volume to surface mapping (mri_vol2surf) using fmriprep outputs

Until now with your help I have figured how to do the most important operations. For example, I do a lot of mri_label2vol to carry roi’s that I draw on the surface back to volume. This requires anat2exf.register.dat in my old pipeline. But looks like it also works fine when I use --identity as the reg method [temp should be the orig.mgz] mri_label2vol --subject sub-01 --hemi rh \ --identity \ --label path/ffa.label \ --temp path/freesurfer/sub-01/mri/orig.mgz \ --o path/ffa_label.nii I coul…

[pettitta]

This has been great! It’s sent me down quite the helpful rabbit hole. The only thing I’m having trouble doing now is viewing the 4d file in freeview. It keeps crashing on me every time I try to view the output of mri_vol2surf. How do you go about checking to see if your transformation actually worked?

Adam

[Ursula_Tooley]

Ah yes. Well…you have to load it as an overlay to a surface–you can’t load the file itself as a surface. Also, you have to load it on the correct res surface (ie fsaverage5 if that’s what you projected to). I had the same issues. Hopefully that helps?