Hi Fidel

Thanks for your reply. 

I’ve traced the error on that line 70 to the “jobPREPAREFIELDMAP” variable, which appears to not have been assigned a value. If I assign a number to that variable (e.g. jobPREPAREFIELDMAP = 0) between lines 69 and 70, then the topup function works fine. But I don’t know whether that value is important for how the topup function runs, or if it just there for logging purposes?

It's not clear why the previous line (69) does not assign an output, but the log suggests a problem in bb_prepare_struct_fieldmap. There are errors reported from that function in the log output from bb_pipeline_struct:

"bb_prepare_struct_fieldmap_MNP_test1" -l /home/cab79/Data/MNP_test1/logs/ -j 3758 $BB_BIN_DIR/bb_structural_pipeline/bb_prepare_struct_fieldmap MNP_test1 
2018-12-16 11:23:59,129 - bb_pipeline_struct - ERROR - Exception type: 	<class 'subprocess.CalledProcessError'> 
2018-12-16 11:23:59,129 - bb_pipeline_struct - ERROR - Exception args: 	(1, '${FSLDIR}/bin/fsl_sub -T 5 -N "bb_prepare_struct_fieldmap_MNP_test1" -l /home/cab79/Data/MNP_test1/logs/ -j 3758 $BB_BIN_DIR/bb_structural_pipeline/bb_prepare_struct_fieldmap MNP_test1') 
2018-12-16 11:23:59,129 - bb_pipeline_struct - ERROR - Exception message: 	Command '${FSLDIR}/bin/fsl_sub -T 5 -N "bb_prepare_struct_fieldmap_MNP_test1" -l /home/cab79/Data/MNP_test1/logs/ -j 3758 $BB_BIN_DIR/bb_structural_pipeline/bb_prepare_struct_fieldmap MNP_test1' returned non-zero exit status 1 
2018-12-16 11:23:59,129 - bb_pipeline_struct - INFO - COMMAND TO RUN: 	${FSLDIR}/bin/fsl_sub -T 90 -N "bb_topup_MNP_test1" -l /home/cab79/Data/MNP_test1/logs/ -j 0 ${FSLDIR}/bin/topup --imain=MNP_test1/fieldmap/B0_AP_PA --datain=MNP_test1/fieldmap/acqparams.txt --config=b02b0.cnf --out=MNP_test1/fieldmap/fieldmap_out --fout=MNP_test1/fieldmap/fieldmap_fout --jacout=MNP_test1/fieldmap/fieldmap_jacout -v 

But, the log outputs from bb_prepare_struct_fieldmap look ok as far as I can tell:

+ numAP=1
+ numPA=1
+ '[' '!' -d MNP_test1/fieldmap ']'
++ /usr/local/fsl/bin/fslval MNP_test1/dMRI/raw/AP.nii.gz dim2
+ numlines='104 '
++ /home/cab79/UK_biobank_pipeline_v_1/bb_pipeline_tools/bb_get_dwell_time MNP_test1/dMRI/raw/AP.nii.gz
+ dtiDwell=0.67
++ bc
++ echo 'scale=4;(0.67 * (104' ' -1.0)) / 1000.0 '
+ topupValue=0.0690
+ cat /dev/null
++ seq 1 1
+ for i in '`seq 1 $numAP`'
+ printf '0 -1 0 0.0690\n'
++ seq 1 1
+ for i in '`seq 1 $numPA`'
+ printf '0 1 0 0.0690\n'
++ /usr/local/fsl/bin/fslval MNP_test1/fieldmap/B0_AP_PA dim3
+ Zslices='72 '
++ expr 72 % 2
+ rem=0

This is also using fsl_sub, but as the topup line seems to work ok (with a dummy value for jobPREPAREFIELDMAP) I assume it is not a problem with fsl_sub. If it's ok to fudge it by assigning an arbitrary value to jobPREPAREFIELDMAP, I can do that for now, but I worry that bb_prepare_struct_fieldmap might not be producing the correct image outputs if it is producing errors.

On a separate note: Further along the pipeline, I think there is an error in the bb_GDC script. On line 97 it says:

${FSLDIR}/bin/fslroi ${InputFile}.nii.gz $WD/${BaseName}_vol1.nii.gz 0 1

But I think it should be without the .nii.gz after InputFile:

${FSLDIR}/bin/fslroi ${InputFile} $WD/${BaseName}_vol1.nii.gz 0 1

At least, I had to remove that for it to run properly.

I now have some further problems with running the gradientunwarp package but will send details in a further message as this one is getting long!

Many thanks
Chris

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