Hi,
I've been noticing this for a while, but it was only when one of our
users updated their FSL to 4.1.5 and asked about it that I looked into
it. We use flschfiletype to convert from Analyze 7.5 to Nifti, it
appears that fsl 4.0.4 used to set the cal_max and cal_min fields and
4.1.? no longer does. This is apparent when viewing images in fslview,
which uses those values to set the starting window levels (sometimes the
image is completely black with the initial levels, sometimes binary
contrast and sometimes about right). We can work around easily enough
with -mul 1 in fslmaths, but I was wondering whether this change was
intentional.
Either way, the problem then appeared again; on running images with
corrected cal_min and cal_max through FIRST, those header values were
unchanged. Since the segmentation classes were lower intensity than the
segmented [0:1000], they load up in fslview very dark. Again, fslmaths
can be used as a workaround, or some scripting with fslcreatehd, but I
was a bit surprised to find fslview uses the fields if they're not set
by other tools.
So, is this a known problem, a non-problem or am I missing something
(e.g. using fslview differently for looking at first segmentations), and
are there any other workarounds for cal_min and cal_max not set?
Thanks,
Ian
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