Issue with topup_datain.txt in PyDesigner Docker (v1.0.0)

[Mohammadmasood1992]

Hello PyDesigner team,

I am running the Docker version (v1.0.0) on my multishell data to obtain DTI and DKI metrics using the following command:

"docker run -it --rm -v /home/mbayat/Documents/sub-01/dMRI:/data dmri/neurodock pydesigner --standard --output /data/dk /data/raw/AP.nii.gz /data/raw/PA.nii.gz --verbos"

However, I encounter the following error:

"topup --imain=topup_in.nii --datain=topup_datain.txt --out=field --fout=field_map.nii.gz --config=/usr/local/fsl/etc/flirtsch/b02b0.cnf --verbose
Part of FSL (ID: "")
topup
Usage:
topup --imain=<some 4D image> --datain= --config= --out=my_topup_results
...
TopupFileIO::TopupDatafileReader:: error reading file topup_datain.txt"

When I inspect the "topup_datain.txt" file, I notice that there is an extra space at the beginning of the first five lines (I’ve added asterisks to indicate the extra space):

*0 -1 0
*0 -1 0
*0 -1 0
*0 -1 0
*0 -1 0
0 1 0
0 1 0
0 1 0

I manually removed the extra space and reran the script using either the --resume or --force flags, but encountered this error:

"mrinfo: [ERROR] output file "/data/dk/dwiec.bvec" already exists (use -force option to force overwrite)"

I also tried deleting the "/data/dk/dwiec.bvec" file and running the script again, but I still get the same "TopupFileIO::TopupDatafileReader:: error reading file topup_datain.txt" error.
Could you please advise on how to resolve this issue?