Hi Bruce and all, Thanks for the suggestion on scaling -- it would be nice if it were consistent, but it varies quite a lot from scan to scan. At the most, about 30 of the top slices are affected, but often the number of affected slices is fewer, and sometimes the spatial extent of the artifact is small enough that the signal intensity of the cortex is unaffected.
Another note that might be of interest is that skull stripping seems to succeed even in severe cases of the artifact. I'm not sure if that could be leveraged to solve the problem. Best, Andrew On Tue, Mar 7, 2017 at 3:50 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Andrew > > wow, that's pretty strange. The only thing I can think of that might > recover this is to put pairs of control points in the white matter, one on > either side of the boundary of your artifact. Or maybe it always affects > the same slices and you can scale them up? I guess it depends on how > variable it is > > cheers > Bruce > > > On Tue, 7 Mar 2017, Andrew D. Davis wrote: > > Hello Freesurfer experts, >> >> I have a dataset in which there is an artifact affecting many subjects. >> The >> problem is a greatly reduced signal at the top of the head. The images >> come >> from a GE scanner and it appears to have been caused by a configuration >> issue in the protocol. Sometimes this artifact impacts the cortical grey >> matter, as in the attached screenshot (showing T1.mgz after this subject >> was >> run through recon-all). In these cases the aseg.mgz is invalid in these >> superior areas, as the mask does not extend into the signal dropout area. >> >> I'm wondering if anyone has an idea for correcting this issue, perhaps by >> adjusting parameters associated with Freesurfer's non-uniformity >> correction >> steps. >> >> Thanks much for any suggestions, >> Andrew Davis >> >> >> Inline image 1 >> >> > _______________________________________________ > 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. > >
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