Hi Doug, Thanks for the quick reply. I actually saw this link before first posting my question but it doesn't quite answer my question. What I want to know is whether the T1.mgz & aseg.mgz files are in an atlas space? if that's the case, it means the segmentation for all my subjects are in the same space and I don't need to convert anything if I want to compare their hippocampal volumes. I'm not quite sure if any sort of registration to an atlas is done in any steps of recon-all or not. I would appreciate if could clarify this for me.
Thanks, -Mojdeh On 12/18/2012 12:18 PM, Douglas N Greve wrote: > Hi Mojdeh, try looking at this doc > http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat > doug > > On 12/18/2012 11:09 AM, Mojdeh Zamyadi wrote: >> Hi all, >> >> I want to segment the hippocampus into head/body/tail in itk SNAP using >> the hippocampus mask that I create from the result of recon-all >> segmentation. My question is, are the T1.mgz and aseg.mgz files in the >> native space of the image or in the atlas space? I know the voxel size >> is different (1x1x1 mm) from the original voxel size (0.49x0.49x0.45), >> but I want to know if the original images are registered to a common >> atlas space or just resampled to a different voxel size. The reason I'm >> asking this, is because I'm doing a group study and I want to make sure >> all my subjects are in the same space so that the segmentation I do is >> accurate for all. >> >> Thanks for your help, >> >> Mojdeh Zamyadi, MSc >> Clinical Research Project Assistant >> The Hospital for Sick Children >> 555 University Avenue >> Toronto ON M5G 1X8 >> >> >> _______________________________________________ >> 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.
