Hi Bruce, Thanks for the clarification. Really appreciate your assistance.
Best, -Prad ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, December 19, 2014 9:45 AM To: Freesurfer support list Subject: Re: [Freesurfer] Clarification regarding group specific average template creation I take it back, mris_make_subject does create the .tifs you would need for mris_register. I still doubt it will change much, but feel free to try it out and let us know how it goes cheers Bruce On Fri, 19 Dec 2014, Bruce Fischl wrote: > Hi Prad. > > 1. Doug can correct me if I'm wrong, but I don't think make_average_subject > creates a new average folding pattern atlas (which would use > mris_make_template). If it does you could use those tifs as a target for > mris_register, but I suspect it won't change much of anything. > > 2. If make_average_subject does call mris_make_template you wouldn't have to. > > 3. I wouldn't treat the longitudinal stuff any differently from the > perspective of atlas creation/target. > > 4,5. No, I don't think this is necessary > > cheers > Bruce > > > On Fri, 19 Dec 2014, Bharadwaj, Pradyumna - (prad) wrote: > >> Hi Bruce, >> >> Thank you so much for the quick response. >> >> I have a few follow up questions based on your suggestion. >> >> 1. I already have a group specific average subject made with >> make_average_subject. So, I can directly use those tif files to re-run >> mris_register ? >> >> 2. What is the purpose of creating a second template after re-registering >> all my subjects to the average? >> >> 3. What would your recommendation be regarding group specific average for >> longitudinal data ? >> >> I know the longitudinal data workflow, creates a within subject average/ >> template. So, >> >> 4. Do I then create a new longitudinal average from all the within >> subject templates? Or, >> >> 5. Do I first create a group specific average for each timepoint, >> re-register the subjects in that timepoint to that average and then >> run the longitudinal processing stream? >> >> Thanks, >> >> -Prad >> >> >> >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Thursday, December 18, 2014 3:46 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Clarification regarding group specific average >> template creation >> >> Hi Prad >> >> no, everything is still ni fsaverage space. You would need to run >> mris_make_template to create a new template, then rerun mris_register >> >> cheers >> Bruce >> >> >> On Thu, 18 Dec 2014, Bharadwaj, >> Pradyumna - (prad) wrote: >> >> > >> > Hello, >> > >> > >> > My question is regarding the registration procedure using a group >> > specific >> > average template. >> > >> > >> > I ran recon-all for my group(with >100 subjects), created an average >> > subject >> > using make_average_subject and then used recon-all qcache by referencing >> > the >> > average template that I just created. I also ran 10,000 iterations of >> > the >> > monte carlo simulation using the above average template for multiple >> > comparisons correction. I plan to use QDEC to analyze my group data. >> > >> > >> > From what I’ve understood so far, during recon-all, each subject is >> > registered to the spherical surface of fsaverage. So, by specifying my >> > average template during the qcache step I’m resampling the data created >> > from >> > the registration with fsaverage onto my own average template. (Is my >> > understanding correct?) >> > >> > >> > I later found this page >> > (https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates ) >> > which >> > outlines a workflow where an average template is created iteratively >> > using >> > the spherical registration parameters of the initial average template. I >> > see >> > that this page was last updated in 2011 and I wanted to know if this >> > still >> > applies to the current version (5.3) >> > >> > >> > If it does apply to the current version, would my workflow be in any way >> > equivalent to the one at the link above? Or would I have to re-register >> > my >> > subjects and re-run all the subsequent steps? >> > >> > >> > I’m quite new to freesurfer and would really appreciate any inputs on >> > this >> > matter. >> > >> > Looking forward to hearing back, >> > >> > -Prad >> > >> > >> > >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ 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 . 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