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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