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Dear Bruce
Thanks for the explanation. Is there a way of turning off the -mprage flag from
the recon-all command? If not I think I can figure out how to run the first
stage taking individual commands from recon-all.cmd.
Paul
Hi Paul
yes, the -mprage flag could definitely cause what you are seeing. It assume
higher CNR and lower SNR in the images (hence bigger class separation between
gray and white), and if used on SPGR it could definitely erode boundaries like
this.
cheers
Bruce
On Fri, 31 Jan 2020, Wright, Paul wrote:
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Dear FreeSurfer experts
I am a relative novice with FreeSurfer. I am reprocessing some older images
with v6.0 that were previously processed with v5.3. In the newer batch, the
GM-WM boundary is wider and the pial boundary is pushed out, but the newer
version does a better job in the hippocampus. I am trying to figure out what
parameters might differ between versions so I can get a cortical
reconstruction as well as hippocampal segmentation. Both batches used plain
vanilla recon-all -all.
The attached figure shows v5.3 on top and v6.0 below, with aseg.mgz over
T1.mgz. I used an example that as well as thin cortex in the new version,
shows a hippocampal error in the older version. (The slices are aligned at
the hippocampus, but the pitch is slightly different so they don't line up
more superiorly.)
>From the T1, it looks like the step that sets white matter to 110 is more
aggressive in 6.0. I looked through recon-all.cmd and noticed both
normalization steps include the -mprage flag in 6.0 not 5.3.Could this be
the why the results differ? (The images are SPGR not MPRAGE.) Looking at
help for mri_normalize it doesn't mention this flag or how to switch it off,
so I'm stuck here. Of course, it might be something else, not the -mprage
flag.
I'd much appreciate any guidance from the list.
Best wishes
Paul
Paul Wright, PhD
Postdoctoral Researcher, Department of Neuroimaging
King's College London
Maurice Wohl Clinical Neuroscience Institute
125 Coldharbour Lane
London SE5 8NU
Desk: +44 20 7848 8579
Mobile: +44 7491 905754
Email: p.wri...@kcl.ac.uk
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