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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:
External Email - Use CautionHi 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
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:
External Email - Use CautionDear 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