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Hi Doug,

I'm still trying to troubleshoot my mris_preproc error: dimension mismatch.

I don't think qcache was run on the CBF images because they were last processed in SPM (working on old dataset made by someone else)...there aren't any smooth fwhm files. Is it possible to run qcache on a nonnative freesurfer file? i.e. recon-all -s <subjid> -qcache -measure CBF.mgh?

Since I don't think this is an option I'm trying to run mri_surf2surf (--srcsubject subjid --srcsurfval subjid/surf/lh.CBF.fwhm10.mgh (ran in to type 3 error when didn't specify the path) --trgsubject fsaverage --trgsurfval lh.thickness.fsaverage.mgh --hemi lh ....should I be using a different target file?

Hopefully this will solve my issue.

Also, is it possible that different FS versions create different vertices? I am remaking my fsaverage with an older FS version to see if that may fix the issue.

Please let me know if my questions are unclear, and I will try to rephrase and add script input/output.

Thanks, Doug P

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Friday, February 15, 2019 8:26 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc error: dimension mismatch

The subject surface probably changed since the last time you ran qcache and now has a different number of vertices. Try re-running qcache for those subjects.

On 2/15/19 2:58 AM, Peters, Douglas G wrote:

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Hi Everyone,

I'm trying to prepare my Cerebral blood flow surface data for mri_glmfit group analysis (qdec doesn't allow you to choose your own subject surface files to analyze, so I figured mri_glmfit is my only option). Quick summary of what I did and where I get stuck:

##########

I made a vol2surf conversion for some subject perfusion images hoping to evaluate CBF as if it were cortical thickness. The original CBF volumes were registered and normalized in SPM and saved as CBF.nii all in same T1 space. I made them into surface files using : mri_vol2surf --mov CBF.nii--regheader SubjectID --hemi rh --projfrac 0.5 --fwhm 10 --o CBF.mgh

I then tried to run:

mris_preproc --fsgd CBF.fsdg \

--cache-in CBF.fwhm10 \

--target fsaverage \

--hemi rh \

--out rh.CBF.10.mgh\

scans through all the subject .mghs

ninputs = # subjects

Checking inputs

"ERROR: dimension mismatch between" the first two surface files in my subject fsdg file

##########

Please help. What should I do to get around this?

Thanks,

DP

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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It turns out I could run qcache on a unique surface file in the subject's <surf> folder. After a few tries with the surface file name it worked.

Using tcsh command line I ran qcache on all of my subjects:

cd your_study_group_data

setenv SUBJECTS_DIR $PWD

foreach i (*)

echo $i

recon-all -subjid $i -qcache -measure CBF.mgh

end

mris_preproc ran on the smoothed output files!

Thanks for your help. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Thursday, February 21, 2019 9:22 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc error: dimension mismatch

If you have a volume and a registration file, you can run mris_preproc with the --iv option. Eg, something like

mris_preproc --fsgd abc.fsgd --target fsaverage --hemi lh \

* --out abc-lh-vol.mgh --iv abc01-func/bold/main/nvr/ces.bhdr abc01-func/bold/register.lta --iv abc02-func/bold/main/nvr/ces.bhdr abc02-func/bold/register.lta --iv abc03-func/bold/main/nvr/ces.bhdr abc03-func/bol/register.lta --iv abc04-func/bold/main/nvr/ces.bhdr abc04-func/bold/register.lta

On 2/20/19 7:20 PM, Peters, Douglas G wrote:

    External Email - Use Caution

Hi Doug,

I'm still trying to troubleshoot my mris_preproc error: dimension mismatch.

I don't think qcache was run on the CBF images because they were last processed in SPM (working on old dataset made by someone else)...there aren't any smooth fwhm files. Is it possible to run qcache on a nonnative freesurfer file? i.e. recon-all -s <subjid> -qcache -measure CBF.mgh?

Since I don't think this is an option I'm trying to run mri_surf2surf (--srcsubject subjid --srcsurfval subjid/surf/lh.CBF.fwhm10.mgh (ran in to type 3 error when didn't specify the path) --trgsubject fsaverage --trgsurfval lh.thickness.fsaverage.mgh --hemi lh ....should I be using a different target file?

Hopefully this will solve my issue.

Also, is it possible that different FS versions create different vertices? I am remaking my fsaverage with an older FS version to see if that may fix the issue.

Please let me know if my questions are unclear, and I will try to rephrase and add script input/output.

Thanks, Doug P

---

*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Friday, February 15, 2019 8:26 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] mris_preproc error: dimension mismatch The subject surface probably changed since the last time you ran qcache and now has a different number of vertices. Try re-running qcache for those subjects.

On 2/15/19 2:58 AM, Peters, Douglas G wrote:

...

    External Email - Use Caution

Hi Everyone,

I'm trying to prepare my Cerebral blood flow surface data for mri_glmfit group analysis (qdec doesn't allow you to choose your own subject surface files to analyze, so I figured mri_glmfit is my only option). Quick summary of what I did and where I get stuck:

##########

I made a vol2surf conversion for some subject perfusion images hoping to evaluate CBF as if it were cortical thickness.The original CBF volumes were registered and normalized in SPM and saved as CBF.nii all in same T1 space.I made them into surface files using : mri_vol2surf --mov CBF.nii--regheader SubjectID --hemi rh --projfrac 0.5 --fwhm 10 --o CBF.mgh

I then tried to run:

mris_preproc --fsgd CBF.fsdg \

--cache-in CBF.fwhm10 \

--target fsaverage \

--hemi rh \

--out rh.CBF.10.mgh\

scans through all the subject .mghs

ninputs = # subjects

Checking inputs

"ERROR: dimension mismatch between" the first two surface files in my subject fsdg file

##########

Please help. What should I do to get around this?

Thanks,

DP

---

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---

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