If you have a registration LTA file (eg, from bbregister), the you can run something like

set gcam = $SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z
set dstreg = $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta
mri_vol2vol --gcam input.nii.gz  reg $gcam $dstreg 0 0 output.nii.gz


On 8/5/2020 9:31 AM, Zollei, Lilla,Ph.D. wrote:
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
 

        External Email - Use Caution        

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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