Hi Everyone,
Back in May I was very excited to learn that there was some movement toward allowing Freesurfer to utilize the higher than 1mm iso. resolutions of some of our structural images, which could be fantastic help in subcortical segmentations. Is this something that is still in the works for the next release?
gratefully,
Joshua
- Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
On Thu, May 31, 2012 at 5:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Joshua
sorry, I haven't found the time to really work on it. I spent a couple of hours and found some problems, but haven't found the time to fix them
Bruce
On Thu, 31 May 2012, Joshua Lee wrote:
Hi Bruce,
I'm just checking in to see how it turned out with the subcortical segmentation using the high resolution images I sent. Best,
Joshua
Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
On Tue, May 15, 2012 at 5:29 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: you need to call mris_make_surfaces directly. It's a bit complicated as you need to intensity normalize and register the hires volume to the surfaces first. I have an example script if anyone is interested, but no one has used it yet but me I don't think (unless Matt Glasser has gotten his version working, which on second thought he probably has)
On Mon, 14 May 2012, Michael Waskom wrote: Hi Bruce, Is there a flag for this on recon-all? áOr do you need to use mri_make_surfaces directly? Best, Michael On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: á á áHi Joshua á á áyes, we already have upgraded mris_make_surfaces to take higher á á áres data á á áand refine the surfaces with it. Haven't tried it on the aseg á á áyet, but if á á áyou upload a sample dataset I could see how hard it is. á á ácheers á á áBruce á á áOn Mon, 14 May 2012, á á áJoshua Lee wrote: á á á> Dear Freesurfers, á á á> á á á> Over the last years, MR imaging technology hasimproved such á á áthat sub 1-mm á á á> isotropic scans can be obtained with good signal to noise á á ácharacteristics. á á á> For example, our lab uses 0.7mm isotropic structural MR á á áimages. I understand á á á> that the Freesurfer pipeline will up-sample these to 1mm á á áisotropic, but it á á á> seems a shame that so much information is left unused which á á ácould be used to á á á> improve the accuracy of sub-cortical and cortical á á ásegmentation. My question á á á> is whether there are any plans at Freesurfer to change the á á áreference á á á> standard resolution from 1mm isotropic, or provide another á á ásolution that can á á á> help researchers make the most of your technology. á á á> á á á> Sincerely, á á á> á á á> á á á> Joshua á á á> - á á á> Joshua á á á> á á á> á á á> ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-
Joshua Lee