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:
1. 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.? 2. 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)? 3. 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.grimm@zi-mannheim.de mailto:oliver.grimm@zi-mannheim.de
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.Grimm@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.grimm@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.
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 koen@nmr.mgh.harvard.eduwrote:
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.Grimm@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.grimm@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
freesurfer@nmr.mgh.harvard.edu
-
Grimm, Oliver -
Joshua Lee -
Koen Van Leemput