Thanks a ton Martin,
can you possibly clue me into where I could find study_average?
best, jon On Nov 6, 2013, at 2:16 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote:
Hi Jon,
passing the --qdec-long flag to mris_preproc will automatically generate the right names (e.g. the .long. directories) and take the data from there. You can pass the study_average vie the --target flag. The default is to use fsaverage which is distributed with FreeSurfer.
So mris_preproc maps the thickness maps to the subject average, while the mris_surf2surf command is for smoothing the stack of thickness maps and generates the …_sm10.mgh file.
Best, Martin
On Nov 6, 2013, at 2:07 PM, Jonathan Holt whatsdac@umich.edu wrote:
FS experts,
I have two questions, when running mris_preproc and mri_surf2surf should I be passing these any of the .long directories created with recon-all -long? As I read through the tutorial I’m missing their significance in the analysis section of the longitudinal stream. It seems like fsaverage is being used (I’m not sure when that was even generated)
Secondly, I see that mris_preproc outputs a thickness.mgh file, but I’m wondering where, in your tutorial examples lh.thickness_sm10.mgh comes from/is located. Found in
mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex —noreshape
best,
jon
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