External Email - Use Caution        

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:

        External Email - Use Caution        

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

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer