Hi all,
I'm trying to run feat on a Linux box here at my lab. I'm doing a higher
level analysis, but it fails early on due to some nifti conversion
errors. The thing is, I've set the FSLOUTPUTTYPE to be Analyze and
there's no nifti data anywhere in my inputs. The following is some of
the error text being produced in the report_log.html:
/usr/local/fsl-4.0.3_64bit/bin/featregapply
/ifs/tmp/pipelnvr/2008March18_12h27m58s818ms/FSF2Pipe.FEATInputDirectories_0-0.feat
/usr/local/fsl-4.0.3_64bit/bin/featregapply
/ifs/tmp/pipelnvr/2008March18_12h27m58s818ms/FSF2Pipe.FEATInputDirectories_0-1.feat
/usr/local/fsl-4.0.3_64bit/bin/featregapply
/ifs/tmp/pipelnvr/2008March18_12h27m58s818ms/FSF2Pipe.FEATInputDirectories_0-2.feat
/usr/local/fsl-4.0.3_64bit/bin/featregapply
/ifs/tmp/pipelnvr/2008March18_12h27m58s818ms/FSF2Pipe.FEATInputDirectories_0-3.feat
/usr/local/fsl-4.0.3_64bit/bin/fslmerge -t bg_image
/ifs/tmp/pipelnvr/2008March18_12h27m58s818ms/FSF2Pipe.FEATInputDirectories_0-0.feat/reg_standard/reg/highres
/ifs/tmp/pipelnvr/2008March18_12h27m58s818ms/FSF2Pipe.FEATInputDirectories_0-1.feat/reg_standard/reg/highres
/ifs/tmp/pipelnvr/2008March18_12h27m58s818ms/FSF2Pipe.FEATInputDirectories_0-2.feat/reg_standard/reg/highres
/ifs/tmp/pipelnvr/2008March18_12h27m58s818ms/FSF2Pipe.FEATInputDirectories_0-3.feat/reg_standard/reg/highres
** ERROR: nifti_convert_nhdr2nim: bad dim[0]
** ERROR (nifti_image_read): cannot create nifti image from header
'/ifs/tmp/pipelnvr/2008March18_12h27m58s818ms/FSF2Pipe.FEATInputDirectories_0-0.feat/reg_standard/reg/highres.hdr'
** ERROR:
nifti_image_open(/ifs/tmp/pipelnvr/2008March18_12h27m58s818ms/FSF2Pipe.FEATInputDirectories_0-0.feat/reg_standard/reg/highres):
bad header info
Error: failed to open file
/ifs/tmp/pipelnvr/2008March18_12h27m58s818ms/FSF2Pipe.FEATInputDirectories_0-0.feat/reg_standard/reg/highres
Cannot open volume
/ifs/tmp/pipelnvr/2008March18_12h27m58s818ms/FSF2Pipe.FEATInputDirectories_0-0.feat/reg_standard/reg/highres
for reading!
Going into the directory mentioned above, I see two files, highres.img
and highres.hdr, which are not Nifti. Why feat insists on interpreting
them as such, I have no clue.
For clarification, I'm executing feat from the following script:
export FSLDIR="/usr/local/fsl-4.0.3_64bit"
. $FSLDIR/etc/fslconf/fsl.sh
export FSLOUTPUTTYPE="ANALYZE"
echo $FSLOUTPUTTYPE
$FSLDIR/bin/feat converted.fsf
Also, fsl.sh sets $FSLOUTPUTTYPE to be ANALYZE, but I set it again just
in case before calling feat.
Any help with regards to this would be fantastic. Everybody in our lab
is super excited to get started with feat on v4.
Thanks,
Arash
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