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
