Hi Jacob,
0.9 vs 1mm shouldn’t change much. If you want to use the T2, then definitely
provide it as “additional volume” eg with segmentHA_T2.sh
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
http://www.jeiglesias.com
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Jacob Bunyamin
<jacob.bunya...@monash.edu>
Date: Thursday, September 19, 2024 at 10:39 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal segmentation on two sets of MRI with
different resolution
External Email - Use Caution
Good afternoon,
I have two sets of MRIs with different resolutions (0.9mm3 and 1mm3 isotropic).
At the moment I ran the hippocampal segmentation on both so I assume that the
volume I obtained from 0.9mm3 was downsampled to 1mm3 after recon-all. I just
read that recon-all allows us to keep the resolution using the -cm flag, the
question is would the volume I obtain after rerun with -cm from 0.9mm3 scans be
comparable with the volume I obtained from the other set (the 1 mm3 scans) or
is it better to keep the downsampled ones?
Some subjects also have high-resolution T2 (0.4x0.4x2 mm3) scans, would running
the recon-all with -cm affect the T1+T2 segmentation result as well?
Thank you very much.
Kind regards,
Jacob
--
Jacob Bunyamin
PhD Student
Department of Neuroscience
School of Translational Medicine
Monash University
E: jacob.bunya...@monash.edu<mailto:jacob.bunya...@monash.edu>
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