External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D.
<dgr...@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-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
> N.,Ph.D. <dgr...@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
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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