Hi Mojdeh Have you checked out Koen van Leemput's hippocampal fled segmentation that you can run through recon-all? It might do what you want automatically. Cheers Bruce
On Dec 19, 2012, at 4:07 PM, Mojdeh Zamyadi <mojde...@gmail.com> wrote: > Hi there, > > Sorry, if my question is confusing. This is what I want to do, I have > two groups of controls and patients and I've already run recon-all on > them. I now want to know the head/body/tail volumes. What I did was: > 1. used "mri_binarize" to get the right and left hippocampal masks from > the cortical segmentation (using label numbers 17, 53) > 2. used "mri_convert" to convert left_hippo.mgz, right_hippo.mgz and > T1.mgz into .nii files. > 3. use itk SNAP to manually segment the total hippocampus (the > freesurfer mask) into head, body and tail. > > now, my questions is regarding the last step. If the individual > segmentations are in the native space, I can't be sure that the > landmarks I'm using for head/body/tail separation is always the same > (since some of the subjects might be in an oblique space). So would you > recommend that I first register the T1 and segmentations all into a > common space? Also, I was wondering if the segmentation is going to > effect the actual volume (since the brain is going to be stretched and > transformed while doing the registration). I hope I made my question > clear and I would greatly appreciate your advice. > > Thanks, > -Mojdeh > > On 12/18/2012 12:58 PM, Bruce Fischl wrote: >> 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 >>> >>> >>> >> >> >> 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. >> > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
