Dear Bruce, I have tested the V6 beta version and the bug with FLAIR normalization seems to be corrected there. Can I patch my 5.3 version to include this bug fix? I suppose V6 beta has many modifications making results from 5.3 and V6 versions incompatible.
However, a new problem in V6 beta appeared: it seems that mris_make_surfaces in V6 beta ignores nsigma_above option. The gray matter regions after FLAIRpial refinement are cut out in high intensity FLAIR areas. Modifying nsigma_above (which helped in 5.3. version) does not have an effect in V6 beta. There is a new entry in log file (not present in 5.3 version): resetting max gray (value depending on set nsigma_above) based on CDF to 168 which supposedly overrides my nsigma_above modification. I have uploaded the subject (FLAIRnorm_not_OK_nsigma_above_8.tar.gz) to your server if you would like to take a look. Regards, Antonin Skoch _____ hmmm, that could be a problem, although the surfaces look pretty good, so maybe not. Try V6 beta and see if it still happens. Or upload the subject and we will try it out cheers Bruce On Fri, 19 Jun 2015, Antonin Skoch wrote: > Dear FreeSurfer experts, > > I encountered possible bug in FLAIR intensity normalization in several > subjects. > See attached screenshots with FLAIR.prenorm.mgz and FLAIR.mgz files. The > "normal intensity" pixels in FLAIR.mgz have intensity around 100, whereas > bright pixels (see FLAIR_after_normalization2.png file) have intensities > above 1000. There are several pixels outside head (seen in > FLAIR_normalization2.png file) with value 32767. > > Regards, > > Antonin Skoch > >
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