External Email - Use Caution Hi! Thanks, Doug and Bruce, for your input. It seems to be a problem with the number of iterations (-n). It is currently hard coded to run 4 times. If I run it only once, grey and white are in a normal range (but there are still inhomogeneities). If I run it twice, grey is at 60 and white is at 100. With every following iteration I loose overall brightness. Caspar
Am Fr., 18. Sept. 2020 um 17:16 Uhr schrieb Douglas Greve < dgr...@mgh.harvard.edu>: > It's been a while since 5.3, but I vaguely remember something like this > happening because there were one or two super bright voxels in the image. > If this is the case, then you can find them and clip them. > > On 9/18/20 10:32 AM, Fischl, Bruce wrote: > > I don’t think adding 100 will work as once it scales everything down that > far you only have a couple of bits of representation in the conformed ( 1 > byte/voxel) images. Maybe someone else can comment on fixing nu_correct? > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> > <freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Caspar M. > Schwiedrzik > *Sent:* Friday, September 18, 2020 5:04 AM > *To:* Freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] mri_nu_correct.mni, mri_normalize extremely dark > output > > > > * External Email - Use Caution * > > Hi! > > I am having some issue at the interface between mri_nu_correct.mni and > mri_normalize, using v5.3. > > Specifically, the output when applying mri_nu_correct to a T1 is quite > dark, with white matter in the range of 15. Contrast is ok. When I apply > mri_normalize to nu, it does not scale the data to white matter 110. This > happens with and without a brain mask, and with various other parameter > choices. > > I am tempted to just add 100 to all voxels. > > Any advice? > > Thank you, > > Caspar > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwMDaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=ZhpOvtsqJWyIIADgnoCpqEqvJtfwbe9j-hCxueDDDSE&s=g4LM5FnVW-kh7YfSBv-jF_jEsOgs1b7iIffuOpMearM&e=> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=ZhpOvtsqJWyIIADgnoCpqEqvJtfwbe9j-hCxueDDDSE&s=g4LM5FnVW-kh7YfSBv-jF_jEsOgs1b7iIffuOpMearM&e=
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