Hi All
,
I am using
mri_convert to convert Siemens 30 direction diffusion data into NIfTII
for
proc. with fsl.
mri_convert does it well except that it is a bit problematic that it
comes
out in neurological
convention. Also the tools is fsl do not seem capable to change the orientation
to
radiological
convention. I want to use a structural cooregistered to the diffusion b0 to
navigate for
placing seeds for
stochastic tract processing. mri_convert takes my Siemens structurals and puts
them in NIfTI
files that are
oriented completely wrong, upside down etcetera. Obviously mri_convert knows how
to read Siemens
structurals ... it's
does it all the time for freefurfer processing. So I take analyze 7.5 format
structurals and it comes
out in radiological
convention and fsl tools are incapable to change these into neurological
convention !
so a bit of a sticky
wicket, of course it would be nice if fsl would support it's own tools for data
inport, but as far as I
know they do not.
NIfTI code from COX et. al. is well.... as he puts it himself Klingon software,
Klingon's that fell on their head anyway.
it is not organized
well enough to spend the time to see if anything usable is
there.
I guess the q-form
or s-form are not set such that the fsl tools can work with 7.5 or mri_convert
produced files.
any way to get
correctly oriented NIfTI structurals or to reorient the diffusion data to
radiological.
cheerio
Greg.