What is the output when you type fslorient <file that would be swapped by
fslview>.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Leonardo Cerliani
Sent: Friday, November 07, 2008 5:24 AM
To: [log in to unmask]
Subject: [FSL] (unwanted) X swap when saving nii.gz reconstructed from
PAR/REC 4.1
hello everyone!
I am experiencing a strange (and potentially dangerous) behavior when saving
nii.gz files
(modified or not) from fslview 3.0: the image is swapped on the X axis. (I
don't know if it
can mean something, but I have no such problem when performing operations
with
fslmaths on the same image.)
Did some of you experienced the same problem?
The images have been reconstructed in nii.gz from PAR/REC 4.1 files by means
of the
dcm2nii commandline utility contained in MRIcroN.
One interesting thing: if I use the fslchfiletype utility to convert the
nii.gz to analyze, and
then back to nii.gz, then I can open/modify/save with fslview, and
everything is alright. I
suspect therefore that it could be some problem with the header generated by
dcm2nii
(which actually if I remember well doesn't still fully support PAR/REC 4.1)
P.S. By the way, if some of you knows some other tool to reconstrut PAR/REC
files, it
would be very welcome.
system specifications:
linux opensuse 10.2
fsl 4.0
fslview 3.0
leonardo
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