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 mojdehzm@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:
- 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.