Hi Bruce, > You can't just change which peak is the WM - lots of things downstream would > fail
That is unfortunate. I've send you the subject files and the raw files via filedrop (per these instructions https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange) On Fri, Jul 29, 2016 at 4:38 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Tom > > it's tough for us to tell without some images or the data. If you upload the > entire subject dir of a subject that failed we will take a look. You can't > just change which peak is the WM - lots of things downstream would fail > > cheers > Bruce > > > > On Fri, 29 Jul 2016, tvg[fs] wrote: > >> Dear community and developers, >> >> I am experiencing issues during the normalization step, converting >> NU.mgz to T1.mgz. Gray matter is falsely recognized as white matter >> and high intensity WM is ignored. The resulting T1.mgz collapses the >> wrong voxels into the 110 bin. >> >> It seems that what mri_normalize assumes a peak in the WM intensity >> distribution that is too low. >> In NU.mgz WM seems centered around 140 not 110. Note that this is not >> due to RF-field inhomogeneities. It is likely of physiological origin >> >> - Is there a way to explicitly tell mri_normalize to use a different >> intensity peak? >> >> I realize that correction can be done with control points, however I >> understand that does not compute a new intensity distribution, but >> merely adds voxels around CPs. This is undesirable since I have >20 >> scans to process. Also this will not correct the falsely tagged GM >> voxels. >> >> I've tried to trick mri_normalize by adjusting NU.mgz intensity by -30 >> (140-30 = 110). This did not give me the wished-for effect. >> - Is it possible to bypass preprocessing steps of mri_normalize before >> collapsing? >> >> - In general it would help if there is some elaboration on the options: >> -no1d, >> -nosnr, >> -gentle, >> -f vs -fonly, >> -prune, >> -g, >> -monkey >> - is [-monkey] just shorthand for [-no1d -n 1]? >> >> Thanks, >> Tom >> >> System: >> Mac OS X 10.10.5 >> freesurfer-Darwin-lion-stable-pub-v5.3.0 >>> >>> mri_normalize --version >> >> stable5 >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
