Hi,
If I use custom TPMs in the traditional Analyze format (.hdr+.img pair)
then SPM5 successfully segments the images, if I first convert the TPMs
to single-file NiFTI using avwchfiletype from FSL, then the segmentation
fails totally.
The original TPMs and the NiFTI versions are indistinguishable in SPM5's
"check reg". SPM5 "display" shows that the originals include an
intensity scaling factor that seems to have been lost by FSL in conversion.
Ironically, the images I am trying to segment *have* been converted to
NiFTI (also with FSL), and the SPM default TPMs are NiFTI anyway
(segmentation with these works). So I would expect this to succeed and
the Analyze version to fail, if anything.
I attach screen-grabs of spm display for the grey matter TPMs, and check
reg for the results (showing from left to right: original, native
grey/white/csf, bias corrected, modulated normalised grey.
My questions: is SPM or FSL (or me!) at fault? How can the (NiFTI)
segmentation results look so dreadful when the TPMs look fine, and the
images are themselves NiFTI? And, less directly related, but still
relevant: why does SPM use such low bit-depth (8bit) TPMs?
Many thanks,
Ged.
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