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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
I don't know, probably an open question. The change in resolution will certainly affect results. Using the higher res (ie, not downsampling to 1mm) will likely give you the best result.
On 9/19/2024 10:38 PM, Jacob Bunyamin wrote:
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.bunyamin@monash.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Jacob Bunyamin jacob.bunyamin@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.bunyamin@monash.edumailto:jacob.bunyamin@monash.edu
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Iglesias Gonzalez, Juan E. -
Jacob Bunyamin