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Dear Lilla,

Thank you for your quick response.

Now I tried using

bbregister --s [SUBJECT] --mov [realignedFunctional.nii] --init-coreg --reg register.dat --bold

and then again

mri_vol2vol --mov [realignedFunctional.nii] --o [CVSrealignedFunctional.nii] --m3z cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z --noDefM3zPath --reg register.dat --targ [realignedFunctional.nii]

The output is a nearly empty volume with only a small non-zero patch far from the center.

Am I missing something?

Kind regards,

Peter

Hi Peter,

Running the currently existing command, implicitly assumes that your fMRI data is in the same spatial coordinate space (with the same resolution) as the norm that you used for mri_cvs_register. You will need to use the --reg flag to input the fmri-2-structural transform.

Best, Lilla

---

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Peter Sperrer <e1226992@student.tuwien.ac.at>
Sent: Wednesday, August 5, 2020 9:17 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mri_cvs_register for fMRI

 

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Dear FreeSurfer experts,

My goal is to morph fMRI (data in voxel space) for best possible intersubject GM-overlap. I am using mri_cvs_register as it seemed like a perfect tool for this.

I have already run recon-all on the anatomical scan (160x239x200 voxels at 1x1x1mm) as well as mri_cvs_register --mov [anatomical] --mni.

The resulting normalized brain (final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz) looks pretty good, maybe except for a remaining piece of skull, which does not seem to have impaired the brain data, though.

Functional data has been ST-corrected, realigned and coregistered to the anatomical data in SPM.

Unfortunately, when I try to morph the fMRI images using

mri_vol2vol --mov [PreprocessedFunctional.nii] --o [MorphedPreprocessedFunctional.nii] --m3z cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z --noDefM3zPath --targ cvs/final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz

I end up with a strangely distorted, cropped and ill-oriented image. The file size and resolution is also enormous.

First of all, do you have any suggestions on what could have gone wrong? Is there a better way than using mri_cvs_register  to normalize fMRI data so gyri and sulci between subjects match?

Since I do not need such high resolution for smoothing and analysis, is there a better way than just down-sampling after the morph?

Please excuse if any of these questions seem to have obvious answers to you, I am rather new to using FreeSurfer.

I have already searched the mailing list archive and did not find a solution to my problem but only a slightly related problem from 2013 (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30673.html)
In the solution it was also hinted that morphing fMRI data might be further supported in the future. Is there a tool or function which has been developed since then?

I appreciate your advice!

Thank you very much!

Kind regards

Peter Sperrer

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