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Nevermind, I solved it. One has to replace '--s subject1' with '--s fsaverage6' in the call to mri_surf2surf. Makes sense.

The lh.fsaverage6.sphere.reg file is not needed.

Tim

On May 28, 2020 at 11:00 AM Tim Schäfer ts+ml@rcmd.org wrote:

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Hi Doug,

thanks for your answer, that worked:

mris_apply_reg --src subject1/surf/rh.thickness --streg subject1/surf/rh.sphere.reg fsaverage6/surf/rh.sphere.reg --trg subject1/rh.thickness.fsaverage6.mgz

I do now want to smooth the data. For an FWHM of 5, I tried (adapted from the recon-all script):

mri_surf2surf --prune --s subject1 --hemi lh --fwhm 5 --sval subject1/surf/lh.thickness.fsaverage6.mgz --tval subject1/surf/lh.thickness.fwhm5.fsaverage6.mgz

This fails with (full output attached): ERROR: dimension inconsistency in source data Number of surface vertices = 149244 Number of value vertices = 40962

The first value is the number of vertices in the original surface, the second one is the fsaverage6 vertex count.

So I think it's once more because I do not have (and did not explicitly set as '--surfreg' in the call to mri_surf2surf) the lh.fsaverage6.sphere.reg file.

From reading the recon-all script, it seems I would need a file equivalent to $FREESURFER_HOME/average/folding.atlas.acfb40.noaparc.i12.2016-08-02.tif to obtain the reg file, but for fsaverage6. I have no idea how to get it.

So I'm stuck. Is there any way I can smooth the data?

Tim

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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On May 27, 2020 at 6:48 PM "Douglas N. Greve" dgreve@mgh.harvard.edu wrote:

It is probably easier if you don't use mris_preproc and run the resampling yourself, eg,

mris_apply_reg --src lh.thickness --streg lh.sphere.reg $SUBJECTS_DIR/fsaverage/surf/lh.sphere.reg --streg $SUBJECTS_DIR/fsaverage/surf/lh.sphere.reg $SUBJECTS_DIR/fsaverage6/surf/lh.sphere.reg --trg lh.thickness.fsa6.mgz

On 5/27/2020 7:06 AM, Tim Schäfer wrote:

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Dear FreeSurfer experts,

I'm trying to resample cortical thickness data onto the fsaverage6 template subject in FreeSurfer v6. I have copied fsaverage6 into my $SUBJECTS_DIR.

I tried the following 2 commands:

• mris_preproc --s subject1 --target fsaverage6 --hemi lh --meas thickness --fwhm 5 --out lh.thickness.fwhm5.fsaverage6.mgh

and alternatively:

• recon-all -s subject1 -qcache -measure thickness -target fsaverage6

Both fail because the file subject1/surf/lh.fsaverage6.sphere.reg is missing (see attached recon-all.log file).

How can I generate the ?h.fsaverage6.sphere.reg file?

I tried: mris_register subject1/surf/lh.sphere fsaverage6/surf/lh.sphere subject1/surf/lh.fsaverage6.sphere.reg

However, that fails as well, see attached file mris_reg_output.txt for the error message.

All the best,

Tim

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany