For #2, make_average_subject will create the .tif file in the output directory. doug
On 06/04/2012 09:06 AM, Bruce Fischl wrote: > Hi Christina, > > 1. Displaying data on your own subjects average can be less misleading > than on our's, particularly if you don't have many subjects. It shows > at least one measure of the true variability/accuracy of the > registration of your subjects. > > 2. To make a study-specific target for the spherical registration you > would need to use mris_make_template to create a .tif file as a > target, then rerun mris_register to register to it. Then rerun > make_average_subject and all the statisticaly analyses using the new > spherical registrations. > > cheers > Bruce > > > On Mon, 4 Jun 2012, Schuster, Christina /DZNE wrote: > >> >> 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 >> >> >> >> > > -- 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
