Hi Mark,
Which FSL version are you using?
Cheers,
Matteo
> On 8 Mar 2019, at 17:17, Mark Pinsk <[log in to unmask]> wrote:
>
> Hi there,
> I'm trying eddy_quad and ran into a problem with the -f option.
> Dataset: I have a 2-shell dataset (11 B0, 50 b=1.25K, 90 b=2.5K) collected once in AP and once in PA using SMS=2.
> If I include the -f option for my topup_fout file, eddy_quad fails. If I exclude -f option, then it runs fine.
>
> Here is the command and terminal output with -f:
> eddy_quad \
>> data-eddy-jac \
>> -idx index.txt \
>> -par acqparams.txt \
>> -m nodif_brain_mask \
>> -b ../analysis-files/eddy-bval-horiz.txt \
>> -g ../analysis-files/eddy-bvec-horiz.txt \
>> -s slspec-sms2.txt \
>> -f topup_fout
> found b-shell of 22 orientations with b-value 0.000000
> found b-shell of 180 orientations with b-value 2500.000000
> found b-shell of 100 orientations with b-value 1250.000000
> !!!Warning!!! NaNs detected in the CNR maps!!!
> Running $FSLDIR/bin/slicer data-eddy-jac.qc/avg_b0_pe0 -i 0 41294.0 -a data-eddy-jac.qc/avg_b0_pe0.png
> Image Exception : #75 :: 3D only method called by higher-dimensional volume.
> libc++abi.dylib: terminating with uncaught exception of type armawrap::AWException: 3D only method called by higher-dimensional volume.
> Traceback (most recent call last):
> File "/usr/local/fsl/bin/eddy_quad", line 52, in <module>
> main(args.eddyBase, args.eddyIdx, args.eddyParams, args.mask, args.bvals, args.bvecs, args.output_dir, args.field, args.slspec, args.verbose)
> File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/eddy_qc/QUAD/quad.py", line 358, in main
> quad_susc.main(pp, data, eddyOutput)
> File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/eddy_qc/QUAD/quad_susc.py", line 44, in main
> fslpy.slicer(data['qc_path'] + "/avg_b0_pe" + str(i), a=data['qc_path'] + "/avg_b0_pe" + str(i) + ".png", i=(0, i_max))
> File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/eddy_qc/utils/fslpy.py", line 88, in slicer
> jobout = check_output(cmd, shell=True)
> File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/subprocess.py", line 336, in check_output
> **kwargs).stdout
> File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/subprocess.py", line 418, in run
> output=stdout, stderr=stderr)
> subprocess.CalledProcessError: Command '$FSLDIR/bin/slicer data-eddy-jac.qc/avg_b0_pe0 -i 0 41294.0 -a data-eddy-jac.qc/avg_b0_pe0.png' died with <Signals.SIGABRT: 6>.
>
> Here it is without the -f option:
> found b-shell of 22 orientations with b-value 0.000000
> found b-shell of 180 orientations with b-value 2500.000000
> found b-shell of 100 orientations with b-value 1250.000000
> !!!Warning!!! NaNs detected in the CNR maps!!!
> Running $FSLDIR/bin/slicer data-eddy-jac.qc/avg_b0 -i 0 40550.0 -a data-eddy-jac.qc/avg_b0.png
> Running $FSLDIR/bin/slicer data-eddy-jac.qc/avg_b1250 -i 0 10855.0 -a data-eddy-jac.qc/avg_b1250.png
> Running $FSLDIR/bin/slicer data-eddy-jac.qc/avg_b2500 -i 0 5330.0 -a data-eddy-jac.qc/avg_b2500.png
> Running $FSLDIR/bin/fslsplit data-eddy-jac.eddy_cnr_maps.nii.gz data-eddy-jac.qc/cnr
> Running $FSLDIR/bin/slicer data-eddy-jac.qc/cnr0000.nii.gz -i 0 41.87 -a data-eddy-jac.qc/cnr0000.nii.gz.png
> Running $FSLDIR/bin/slicer data-eddy-jac.qc/cnr0001.nii.gz -i 0 2.63 -a data-eddy-jac.qc/cnr0001.nii.gz.png
> Running $FSLDIR/bin/slicer data-eddy-jac.qc/cnr0002.nii.gz -i 0 3.06 -a data-eddy-jac.qc/cnr0002.nii.gz.png
>
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