I have been working through the topup and eddy tutorials. I have successfully run topup and eddy on the tutorial data and my own data (FSL 5.0.09, Linux distribution). The command I am running is
eddy --imain=dti.nii.gz --mask=bet.mean.b0.dti_mask.nii.gz --index=index.txt --acqp=dti_acqparams.txt --bvecs=dti.bvec --bvals=dti.bval --out=../01-eddy/my_eddy_output --topup=topup -v --repol
The only issue that I found is when I started looking closely at the eddy output. According to the documentation I expecting to see the following output files in the directory ../01-eddy/:
my_eddy_output.nii.gz
my_eddy_output.eddy_outlier_report
my_eddy_output.eddy_parameters
my_eddy_output.rotated_bvecs
my_eddy_output.eddy_movement_rms
my_eddy_output.eddy_restricted_movement_rms
my_eddy_output.eddy_post_eddy_shell_alignment_parameters
my_eddy_output.eddy_outlier_map
my_eddy_output.eddy_outlier_n_stdev_map
my_eddy_output.eddy_outlier_n_sqr_stdev_map
my_eddy_output.eddy_outlier_free_data.nii.gz
The only files that are produced in the ../01-eddy/ directory are
my_eddy_output.nii.gz
my_eddy_output.eddy_outlier_report
my_eddy_output.eddy_parameters
Based upon my previous experience I know I am doing something wrong. I just can't figure out what it is. I have read the documentation and haven't noticed a flag that I need to set. I changed the --out to save files to the current directory that didn't change anything. I even downloaded and installed a fresh version of FSL (05.00.09). I know people have started using FSL 5.00.10 but when I installed it using the fslinstaller.py script it downloaded 05.00.09. I have confirmed that I am using the corrected version of FSL by checking the FSL_DIR. I scoured the mailing list and couldn't find anyone reporting a similar problem.
Any suggestions or insight you could provide would be greatly appreciated.
Thanks for your help
Bob
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