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 > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
