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Thank you very much both of you for your answers.
The co-registration looks fine to me.
Apologies for causing confusion, [realignedFunctional.nii] is the functional volume which has previously been ST-corrected and realigned (motion corrected). (This should be okay as input, shouldn't it?)
When I redid the mri_vol2vol - step I also had [realignedFunctional.nii] as target, though, which I think caused the empty volume.
Now I used
mri_vol2vol --mov [realignedFunctional.nii] --o [CVSrealignedFunctional.nii] --m3z cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z --noDefM3zPath --reg register.lta --targ cvs/final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz
and it seems to have worked.
Thanks again!
Best,
Peter
Am 05.08.2020 um 17:56 schrieb Douglas N. Greve:
Also, use the .lta output of bbregister instead of the .dat output
On 8/5/2020 11:46 AM, Zollei, Lilla,Ph.D. wrote:
Hi Peter, Have you checked the output from bbregister? Did the registration look accurate? Also, the --mov volume should be the functional volume (not the realigned one) 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 11:28 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] mri_cvs_register for fMRI
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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
Am 05.08.2020 um 15:31 schrieb Zollei, Lilla,Ph.D.:
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 mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Peter Sperrer e1226992@student.tuwien.ac.at mailto:e1226992@student.tuwien.ac.at *Sent:* Wednesday, August 5, 2020 9:17 AM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto: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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