Re: [Freesurfer] mri_normalize, 110 is too dark
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 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
[Freesurfer] mri_normalize, 110 is too dark
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] mri_watershed -brain_atlas undocumented?
- This is a repost. It seems it did not come trough yesterday. Apologies if this becomes a double post - Hi all, I noticed that during skull stripping the standard recon-all pipeline uses option "-brain_atlas" in the routine "mri_watershed". However documentation of this argument cannot be found in the help section or on the website. mri_watershed --help | less -p atlas https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed?highlight=(atlas) Is this an undocumented flag or simply a synonym for "-atlas"? Does the "-brain_atlas" flag take an extra argument to specify the atlas? Thanks, Tom Specs: Mac OS X 10.8.5 freesurfer-Darwin-lion-stable-pub-v5.3.0 $ mri_watershed --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] mri_watershed -brain_atlas undocumented?
Hi all, I noticed that during skull stripping the standard recon-all pipeline uses option "-brain_atlas" in the routine "mri_watershed". However documentation of this argument cannot be found in the help section or on the website. mri_watershed --help | less -p atlas https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed?highlight=(atlas) Is this an undocumented flag or simply a synonym for "-atlas". Does the "-brain_atlas" flag take an extra argument to specify the atlas? Thanks, Tom Specs: Mac OS X 10.8.5 freesurfer-Darwin-lion-stable-pub-v5.3.0 > mri_watershed --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.