Hi pfannmoe that page looks pretty good to me. YOu need to create a new folding atlas which we typically store in .tif format using mris_make_template. This is usually done by picking one subject, registering all your subjects to that template (.tif file), recreating the template, reregistering and so on. Usually this converges after 2-3 rounds.
cheers Bruce On Fri, 1 Apr 2016, pfannmo...@uni-greifswald.de wrote: > Dear Experts, > > I am currently working with the non-linear FreeSurfer normalization. > We have a small group of subjects N = 12 and in each brain we > identified a single position with a fMRI localizer. The task is a > group comparison of the individual results for this position. > Therefore, the coordinates of each position in FSaverage was > determined using mri_label2label. The radius of the region is an > important quantity in my investigations. A smaller radius would help > me a lot in my data processing. I tried to decrease the radius by > generating a new group space template from my 12 subjects with > make_average_subject. Then I used mri_label2label to determine the > coordinates in the new group space template. Unfortunately, there > was no difference in the radius. The intention behind this procedure > was to achieve an improved normalization of the subjects. I have read > much about this topic in the mailing list, but there are many details > in the processing which I am not yet aware of. So, my question is if > I proceeded the best possible way or if there is a better alternative > to improve the normalization. Would it help to generate a new template > as outlined in the second part on this web tutorial (chapter: Creating > a registration template from scratch): > > https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates > > or do I need to use mris_register with my new template and my 12 > subjects instead of mri_label2label in order to benfit from my new > template as generated by make_average_subject (also outlined in the > web tutorial in the chapter: Creating a registration template > initialized with FreeSurfer template)? > > Even a small decrease in the radius would help to improve my results. > > Thanks in advance > > pfannmoe > > > > > > > > > _______________________________________________ > 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 . 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.
