Question about command line FIB file construction- unknown eddy error

[Rebecca Roth]

I am using the following code to attempt to generate FIB files through command line across many subjects. I already successfully created the SRC files.

export FSLDIR="/home/lambda/fsl/6.0"
source ${FSLDIR}/etc/fslconf/fsl.sh

FileDir='/media/lambda/Imaging_XFS/test/raw'
Output_Dir='/media/lambda/Imaging_XFS/test/derivatives/DSI'

cases=$(ls ${FileDir} | grep "sub-*")
method=1
for c in ${cases}; do
    input_src="${Output_Dir}/${c}/ses-pre/dwi/*_dwi.src.gz"
    output_fib="${Output_Dir}/${c}"

    echo ${input_src}
    ~/Documents/Applications/dsi-studio/dsi_studio --action=qc --source="${input_src}"
    ~/Documents/Applications/dsi-studio/dsi_studio --action=rec --source="${input_src}" --cmd="[Step T2][Corrections][EDDY]" --method=${method} --param0="1.25" --output="${output_fib}"
done

However, I am getting an unknown eddy error.

+ DSI Studio version: Chen"陳" command line
| DSI Studio version: Chen"陳"
| action=rec
| source=/media/lambda/Imaging_XFS/test/derivatives/DSI/sub-EMOP0096/ses-pre/dwi/*_dwi.src.gz
| loop=/media/lambda/Imaging_XFS/test/derivatives/DSI/sub-EMOP0096/ses-pre/dwi/*_dwi.src.gz
| + processing loop
| | searching *_dwi.src.gz in directory /media/lambda/Imaging_XFS/test/derivatives/DSI/sub-EMOP0096/ses-pre/dwi
| | found 1 files.
| | /media/lambda/Imaging_XFS/test/derivatives/DSI/sub-EMOP0096/ses-pre/dwi/*_dwi.src.gz->/media/lambda/Imaging_XFS/test/derivatives/DSI/sub-EMOP0096/ses-pre/dwi/sub-EMOP0096_ses-pre_dir-AP_dwi.src.gz
| | action=rec
| | + run rec
| | | source=/media/lambda/Imaging_XFS/test/derivatives/DSI/sub-EMOP0096/ses-pre/dwi/sub-EMOP0096_ses-pre_dir-AP_dwi.src.gz
| | | + open SRC file
| | | | using index file for accelerated loading:/media/lambda/Imaging_XFS/test/derivatives/DSI/sub-EMOP0096/ses-pre/dwi/sub-EMOP0096_ses-pre_dir-AP_dwi.src.gz.idx
| | | | + opening sub-EMOP0096_ses-pre_dir-AP_dwi.src.gz
| | | | |_1.342 s
| | | |_2.212 s
| | | + reconstruction parameters:
| | | | method=1
| | | | odf_resolving=0
| | | | record_odf=0
| | | | dti_no_high_b=1
| | | | check_btable=0
| | | | other_output=fa,ad,rd,md,iso,rdi,nrdi
| | | | r2_weighted=0
| | | | thread_count=24
| | | | param0=1.25
| | | | param1=3000
| | | | param2=0.05
| | | | template 0:"ICBM152_adult.QA.nii"
| | | | template 1:"C57BL6_mouse.QA.nii"
| | | | template 2:"dHCP_neonate.QA.nii"
| | | | template 3:"INDI_rhesus.QA.nii"
| | | | template 4:"Pitt_marmoset.QA.nii"
| | | | template 5:"WHS_SD_rat.QA.nii"
| | | | template=0
| | | |_0 ms
| | | + specify mask
| | | | mask=1
| | | |_0 ms
| | | + preprocessing
| | | | preprocessing=0
| | | | motion_correction=0
| | | |_0 ms
| | | + additional processing steps
| | | | cmd=[Step T2][Corrections][EDDY]
| | | | + [Step T2][Corrections][EDDY]
| | | | | run eddy
| | | | | eddy without topup
| | | | | get the bounding box for speeding up topup/eddy
| | | | | trim "sub-EMOP0096_ses-pre_dir-AP_dwi.src.gz" for eddy
| | | | | range: (0,0,0) to (128,128,80)
| | | | | + saving
| | | | | |_48.442 s
| | | | | + saving
| | | | | |_7 ms
| | | | | FSL installation found at /home/lambda/fsl/6.0
| | | | | run /home/lambda/fsl/6.0/bin/eddy
| | | | | path:/media/lambda/Imaging_XFS/test/derivatives/DSI/sub-EMOP0096/ses-pre/dwi
| | | | | --imain=sub-EMOP0096_ses-pre_dir-AP_dwi.src.gz.nii.gz
| | | | | --mask=sub-EMOP0096_ses-pre_dir-AP_dwi.src.gz.mask.nii.gz
| | | | | --acqp=sub-EMOP0096_ses-pre_dir-AP_dwi.topup.acqparams.txt
| | | | | --index=sub-EMOP0096_ses-pre_dir-AP_dwi.src.gz.index.txt
| | | | | --bvecs=sub-EMOP0096_ses-pre_dir-AP_dwi.src.gz.bvec
| | | | | --bvals=sub-EMOP0096_ses-pre_dir-AP_dwi.src.gz.bval
| | | | | --out=sub-EMOP0096_ses-pre_dir-AP_dwi.src.gz.corrected
| | | | | --verbose=1
| | | | | eddy cannot process this data:Unknown error
| | | | |_49.174 s
| | | | ERROR:Unknown error
| | | |_49.174 s
| | |_51.432 s
| |_51.432 s
|_51.435 s
Warning: --output is not used. Please check command line syntax.

Any idea what is going on?

Thank you in advance.

Rebecca W. Roth

Emory University

[Frank Yeh]

Are you able to run eddy directly from the command line?
This may help rule out possible cause of error.