Hi Mojdeh they are not in atlas space and the volumes are for that subject, so you shouldn't have to do anything if I understand you correctly
cheers Bruce On Tue, 18 Dec 2012, 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 >>> >>> > > _______________________________________________ > 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.
