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 <whats...@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 <mreu...@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 <whats...@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 >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> --------------------------------- >> 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: >> mreu...@nmr.mgh.harvard.edu >> reu...@mit.edu >> Web : http://reuter.mit.edu >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. > --------------------------------- 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: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu
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