Hi, many thanks for your help! Unfortunately, I still have some questions:
1) Why would someone only want to display the results on a cohort-specific average, but not use that average for calculation? 2) So if I want to use my cohort-specific average for calcuation of the cortical thickness and I registered all subjects on that, do I then still have to calculate a newnew make_average_subject as it is described on the SurfaceRegAndTemplated page? What is the reason behind that? If I should do it, what flags would mris_preproc need: the --target newnewtemplate and the surfreg newtemplate.sphere.reg? Best wishes, Christina _______________________________________ Von: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Gesendet: Freitag, 1. Juni 2012 17:44 An: Bruce Fischl Cc: Schuster, Christina /DZNE Betreff: Re: AW: [Freesurfer] using own average subject If all you want to do is display it on your average subject, then you can pass fsaverage to mris_preproc and then just display it on your cohort-specific average. doug On 06/01/2012 11:37 AM, Douglas N Greve wrote: > Hi Christina, if you want to use the registration to your new > template, then you need to run mris_register on each subject to > register to the new template. You can actually do this with surfreg, > something like: > > foreach subject (subj1 subj2) > surfreg --s $subject --t newtemplate --lh > end > > This will create $subject/surf/lh.newtemplate.sphere.reg > > You can then run > > mris_preproc --target newtemplate --surfreg newtemplate.sphere.reg ... > > Note that the surfreg cmd above will take about an hour for each subject > > doug > > > > > On 06/01/2012 11:05 AM, Bruce Fischl wrote: >> Hi Christina >> >> you should cc the list so others (Doug!) can answer. The purpose of >> mris_register is to bring your subjects into a common surface-based >> coordinate system. fsaverage lives in that space, but so will the >> average that you make >> >> cheers >> Bruce >> >> >> On Fri, 1 Jun 2012, Schuster, Christina /DZNE wrote: >> >>> Hi Bruce, >>> >>> just to be sure that I understood it correctly: >>> >>> I just use make_average_subject to create my template and then I use >>> mris_preproc --target newtemplate and not further --surf-reg >>> specification. >>> Then after mri_glmfit --surf newtemplate ... I have my final results?! >>> >>> So what is the purpose of the mris_register command? >>> >>> Many thanks for your help. >>> Best wishes >>> Christina >>> >>> ________________________________________ >>> Von: Bruce Fischl [fis...@nmr.mgh.harvard.edu] >>> Gesendet: Donnerstag, 31. Mai 2012 20:39 >>> An: Schuster, Christina /DZNE >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Betreff: Re: [Freesurfer] using own average subject >>> >>> Hi Christina, >>> >>> the new template will already be in the same target space as fsaverage >>> since you used the sphere.reg to create it. Just use it as a >>> background for >>> your group results. >>> >>> cheers >>> Bruce >>> >>> On Thu, 31 May 2012, Schuster, >>> Christina /DZNE wrote: >>> >>>> Dear FreeSurfer experts, >>>> >>>> I am trying to create an average subject based on a matched >>>> subsample (2 different scanners, patients and healthy controls). >>>> >>>> I successfully ran make_average_subject receiving a "newtemplate". >>>> Now I am unsure how to proceed: >>>> >>>> As far as I understand it, according to the SurfaceRegAndTemplates >>>> page >>>> (http://surfer.nmr.mgh.harvard.edu//fswiki/SurfaceRegAndTemplates) >>>> I should use mris_register for each subject from my subsample >>>> receiving ?h.sphere.reg.newtemple files with which I should make >>>> again an average subject, let's call it "newnewtemplate". >>>> >>>> Is that correct? >>>> >>>> Now, if I want to assemble the data into common space using >>>> mris_preproc: what do I need to specify? >>>> Would --target be the newtemplate or newnewtemplate? Do I need to >>>> specifiy the --surf-reg as well? >>>> >>>> >>>> On the other hand, I read in one of your tutorials that I only need >>>> to run make_average_subject receiving a "newtemplate" which I then >>>> specify using mris_preproc as --target and that --surf-reg is not >>>> needed. >>>> >>>> >>>> So what would be the correct way to use my own template for the >>>> group analysis? >>>> >>>> Many thanks for you help! >>>> >>>> Best wishes >>>> Christina >>>> >>>> >>> >>> 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. >>> >>> >>> >> >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
