External Email - Use Caution Hi Bruce,
Thanks for your response. From what I read on the wiki (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) the switch in on by default since freesurfer6.0 (but that doesn’t seem to be the case in 5.3). At any rate we use the BRAVO sequence (on a GE MRI) and it also has an inversion pulse (also CNR isn’t as good as in a MPRAGE). Best Antonin On 3 Sep 2019, at 15:44, Bruce Fischl <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>> wrote: Hi AR 1. mprage in general has higher CNR and lower SNR than non inversion-prepared T1w sequences like FLASH. THe -mprage switch takes advantage of this to loosen the intensity gradient threshold in the region filling of the wm. 2. If you just leave out the -mprage switch it will revert to the default behavior cheers Bruce On Tue, 3 Sep 2019, Rovai Antonin wrote: External Email - Use Caution Hello, From the ReconAllTable (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) I see that the mri_normalize step (producing the T1.mgz file) has the -mprage option. I have two questions: 1. What is this option doing exactly? There is no description in the mri_normalize man page (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize); similarly, the CLI help doesn’t mention this option. 2. How do I change this when launching a ReconAll without re-writing a custom pipeline? (For context our T1 is not MPRAGE and we had some segmentation issues so this is an attempt to debug this). Thanks for you help AR Hôpital Erasme Lien vers Disclaimer [Hôpital Erasme] Lien vers Disclaimer<http://www.erasme.ulb.ac.be/email-disclaimer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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