I had run eddy using the bids version of FSL.

Then at the command line on Mac OSX Mojave, I ran eddy_quad on a set of subjects:

>eddy_quad data -idx index_AP.txt -par acqp_AP.txt -m nodif_brain.nii.gz -b bvals

This seemed to run successfully, producing:

data.qc

avg_b0.png

avg_b1000.png

qc.json

qc.pdf

Next I tried to run eddy_squad:

I created a text file myquads containing a line for each subject's eddy_quad output:

sub-0777/dwi/data.qc

sub-1004/dwi/data.qc

sub-1007/dwi/data.qc

sub-1010/dwi/data.qc

sub-1011/dwi/data.qc

sub-1012/dwi/data.qc

sub-1013/dwi/data.qc

sub-1015/dwi/data.qc

sub-1016/dwi/data.qc

sub-1017/dwi/data.qc

sub-1018/dwi/data.qc

sub-1019/dwi/data.qc

sub-1020/dwi/data.qc

sub-1021/dwi/data.qc

sub-1022/dwi/data.qc

Next I called eddy_squad on that text file like so:

[feckless:derivatives: 608] $ eddy_squad myquads

Generating group database...

Traceback (most recent call last):

File "/usr/local/fsl/bin/eddy_squad", line 40, in <module>

main(args.list, args.grouping, args.group_db, args.update, args.output_dir)

File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/eddy_qc/SQUAD/squad.py", line 80, in main

db = squad_db.main(out_dir + '/group_db.json', 'w', sList)

File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/eddy_qc/SQUAD/squad_db.py", line 42, in main

raise ValueError(qc_json + ' does not appear to be a valid qc.json file')

ValueError: sub-0777/dwi/data.qc /qc.json does not appear to be a valid qc.json file

Any suggestions would be appreciated!

Thanks,

Dianne

Dianne Patterson, Ph.D.

Research Scientist
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University of Arizona
Speech and Hearing Science 314

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(Just East of Harvill)

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