OH,
I see, then how would I generate my own study average, if I wanted to do so?
On Nov 6, 2013, at 2:48 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote:
Hi Jon,
that is just a placeholder, indicating that this can be your own average in a real study. You can simply use 'fsaverage' for it, now.
Best, Martin
On Nov 6, 2013, at 2:22 PM, Jonathan Holt whatsdac@umich.edu wrote:
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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Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
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Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu