I think many have better scans than 1mm. Right now I'm using 0.7mm iso with decent snr, and am collecting 2 scans (about 7 min each), and on most slices I can see internal structural detail. It does seem a shame that all this detail is not used for hippo-subfield segmentation. - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
On Tue, Feb 7, 2012 at 11:38 AM, Koen Van Leemput <k...@nmr.mgh.harvard.edu>wrote: > Hi Oliver, > > You're right: internally we're upsampling the images to 0.5mm > isotropic resolution, so if you had acquired 0.5mm isotropic images > from the start, that would actually be much better (provided you don't > simply trade off SNR for increased image matrix size). The catch with > this is that the scripts I put in FreeSurfer will only work out of the > box on FreeSurfer-reformatted 1mm resolution, so you'd need to tweak > things a bit to get it working. > > Hope this helps, > > Koen > > > > On Thu, Feb 2, 2012 at 3:46 AM, Grimm, Oliver > <oliver.gr...@zi-mannheim.de> wrote: > > > > > > Dear FreeSurfer-User, > > > > > > > > some of my questions are mentioned in some older postings, but I still > > struggle with some basic questions. We are planning to use the new > > hippocampal subfield segmentation of FS 5.1 with 3 T Siemens TRIO with 32 > > channel head coil. Still, I do not fully understand how to optimize our > > image processeing pipeline: > > > > Freesurfer works internally with 1x1x1 mm3 but the hippocampal segmenat > uses > > a higher res. of 0.5 x 0.5 x 0.5 mm3. So should we instead use a higher > > resolution for the hippocampal subfield seg.? > > I understand that the recent FS version is not working well with high > > resolution images, e.g. the atlases are not provided in a higher res, > > however the hippocampal subfield segmentation seems to make use of > > aseg.stats. So is is possible at all to use the FS-pipleine in this case > > (hippocampal subfields)? > > Instead of using a high resolution image, we could average over several > > pictures. When I tried this, I had the visual impression, that there was > > almost no gain in this, the volume estimates were bouncing within a > range of > > 10% but did not converge when averaging from scan 1-5 to a specific > value. > > So is it necessary for a good quality to average images when using > > hippocampal subfield segmentation ? > > > > Thanks for your efforts! > > > > Best, > > > > > > > > > > > > Dr. med. Oliver Grimm > > Zentralinstitut für Seelische Gesundheit > > > > www.zi-mannheim.de > > > > SNiP | Systems Neuroscience in Psychiatry > > > > 68159 Mannheim > > > > Germany > > > > > > > > Tel: +49-621-1703-6341 > > Fax: +49-621-1703-6305 > > email oliver.gr...@zi-mannheim.de > > > > > > _______________________________________________ > > 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 >
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