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 <mreu...@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 <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
_______________________________________________ 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.
