Dear FSL Experts,
After successfully installing the latest version of FSL (v6.0.0), I get the following error message when trying to run 'eddy_qc' (I've included the full command and output here):
/Research/ScientificSoftware/FSL/fslpython/envs/fslpython/bin/eddy_quad dwi.eddy -idx index.txt -par acqparams.txt -m mask.nii.gz -b bvals.bval -g bvecs.bvec -o eddyqc -f topup_results_field.nii.gz -s /study/dean_k99/Studies/hartwell/ProcessingCode/slice_order_file.txt -v
found b-shell of 12 orientations with b-value 0.000000
found b-shell of 9 orientations with b-value 350.000000
found b-shell of 18 orientations with b-value 800.000000
found b-shell of 36 orientations with b-value 2000.000000
RMS movement estimates file detected
Eddy parameters file detected
Eddy s2v movement file detected
(array([ 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
36, 37, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57,
58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
75, 76, 77, 78]),)
Outliers outuput files detected
CNR outuput files detected
Eddy residuals file detected
Topup fieldmap file detected
Running $FSLDIR/bin/slicer eddyqc/avg_b0_pe0 -i 0 1759.0 -a eddyqc/avg_b0_pe0.png
Image Exception : #75 :: 3D only method called by higher-dimensional volume.
libc++abi.dylib: terminating with uncaught exception of type armawrap::AWException: 3D only method called by higher-dimensional volume.
Traceback (most recent call last):
File "/Research/ScientificSoftware/FSL/fslpython/envs/fslpython/bin/eddy_quad", line 52, in <module>
main(args.eddyBase, args.eddyIdx, args.eddyParams, args.mask, args.bvals, args.bvecs, args.output_dir, args.field, args.slspec, args.verbose)
File "/Research/ScientificSoftware/FSL/fslpython/envs/fslpython/lib/python3.6/site-packages/eddy_qc/QUAD/quad.py", line 358, in main
quad_susc.main(pp, data, eddyOutput)
File "/Research/ScientificSoftware/FSL/fslpython/envs/fslpython/lib/python3.6/site-packages/eddy_qc/QUAD/quad_susc.py", line 44, in main
fslpy.slicer(data['qc_path'] + "/avg_b0_pe" + str(i), a=data['qc_path'] + "/avg_b0_pe" + str(i) + ".png", i=(0, i_max))
File "/Research/ScientificSoftware/FSL/fslpython/envs/fslpython/lib/python3.6/site-packages/eddy_qc/utils/fslpy.py", line 88, in slicer
jobout = check_output(cmd, shell=True)
File "/Research/ScientificSoftware/FSL/fslpython/envs/fslpython/lib/python3.6/subprocess.py", line 336, in check_output
**kwargs).stdout
File "/Research/ScientificSoftware/FSL/fslpython/envs/fslpython/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '$FSLDIR/bin/slicer eddyqc/avg_b0_pe0 -i 0 1759.0 -a eddyqc/avg_b0_pe0.png' died with <Signals.SIGABRT: 6>.
When I check the "avg_b0_pe0" image that gets created, I find that it is a 4D nifti image of all the b0s, rather than the average image. Any suggestions on how to fix this error?
Thank you!
Doug Dean
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