No, they are not in any atlas space. The space is "native" in that 1mm in the image represents 1mm in the subject's brain. Therefore, you can directly compare the hippo volume across subjects. doug
On 12/18/2012 12:59 PM, Mojdeh Zamyadi wrote: > 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 >>> >>> > > -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
