Dear FSLers,
when running fsl_anat, we had the following error message:
$ fsl_anat -i tmp
Fri Nov 23 23:05:57 EST 2012
Reorienting to standard orientation
Fri Nov 23 23:06:01 EST 2012
Automatically cropping the image
WARNING!!!! Multiple image files detected:
T1_fullfov.nii T1_fullfov.nii.gz
STOPPING PROGRAM
Could not open matrix file T1_nonroi2roi.mat
Cannot read input-matrix
===============================
under the tmp.anat directory:
$ ls
log.txt T1_fullfov.nii.gz T1_fullfov.nii T1_orig.nii T1_std2orig.mat
T1_fullfov.nii T1_orig2std.mat T1_roi.log
There are indeed two files having the same name T1_fullfov.nii and T1_fullfov.nii.gz.
The contents of the log.txt file:
Script invoked from directory = /data/public/tmpRun
Output directory = tmp.anat
Input image is tmp
/share/apps/fsl/5.0.1/bin/imcp T1 T1_orig
/share/apps/fsl/5.0.1/bin/fslreorient2std T1
/share/apps/fsl/5.0.1/bin/convert_xfm -omat T1_std2orig.mat -inverse T1_orig2std
.mat
/share/apps/fsl/5.0.1/bin/fslreorient2std T1 T1
/share/apps/fsl/5.0.1/bin/immv T1 T1_fullfov
/share/apps/fsl/5.0.1/bin/robustfov -i T1_fullfov -r T1 -m T1_nonroi2roi.mat
/share/apps/fsl/5.0.1/bin/convert_xfm -omat T1_roi2nonroi.mat -inverse T1_nonroi
2roi.mat
What is the problem? Thank you very much.
Rgds,
Jiyang
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