Thank you Martin, This is more than enough.
Jon On Nov 6, 2013, at 3:42 PM, Martin Reuter <mreu...@nmr.mgh.harvard.edu> wrote: > Hi Jon, > > Usually you would select a specific subject to be the target, sometimes that > subject is in the mid age range, etc. Also sometimes people remove that > subject from the study to not introduce a bias. > > In most cases, however, people simply use fsaverage unless they have a reason > to switch. > > I don't know how you create your own 'average' surface. Maybe someone else > can answer that. > > Best, Martin > > > On 11/06/2013 02:57 PM, Jonathan Holt wrote: >> 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 >> > > -- > Martin Reuter, Ph.D. > 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.
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