ERROR ]..... B0 threshold is not a valid integrer: DEFAULT

[hoptman]

• What is the current behavior?
• Please provide the steps to reproduce and if possible a minimal demo of the problem
• What is the expected behavior?
• Please tell us about your computing environment:
• Other information
  I am trying to run -proc_dwi. I have a *.bval file consisting of b=5, b=1495, and b=1500. There are no b=0 images.

When I run the docker command (v0.2.0) docker run -ti --rm -v pwd/bids_data:/bids -v pwd/micapipe:/out -v pwd/micapipe_tmp:/tmp -v /mnt/software/freesurfer/license.txt:/opt/licence.txt micalab/micapipe:v0.2.0 -bids /bids -out /out -fs_licence /opt/licence.txt -threads 3 -sub -ses ses-BAS1 -proc_dwi -dwi_main /mnt/home2/Rockland_sample/bids3/sub-/ses-BAS1/dwi/_ses-BAS1_dwi.nii

I get the message [ERROR].... B0 threshold is not a valid inegrer: DEFAULT

I'm not sure how to get around this, and am stuck.

I am running on a server with Ubuntu 20.04

[rcruces]

Hello, first of all sorry for the late reply. it looks like the arguments are misreaded by bash because -dwi_main is not mounted correctly. If your dataset is BIDS I think the correct code should be something like this:

docker run -ti --rm \
-v pwd/bids_data:/bids \
-v pwd/micapipe:/out \
-v pwd/micapipe_tmp:/tmp \
-v /mnt/software/freesurfer/license.txt:/opt/licence.txt micalab/micapipe:v0.2.0 \
-bids /bids -out /out \
-fs_licence /opt/licence.txt \
-threads 3 -sub -ses ses-BAS1 \
-proc_dwi -dwi_main  /bids/sub-/ses-BAS1/dwi/_ses-BAS1_dwi.nii

Also it seems that your subject argument is empty. -sub is a mandatory argument. It depends on the structure of your dataset naming.

[rcruces]

Did it work? I will close this issue for now. If you need further help please don't hesitate and re-open it.

best

[hoptman]

Did it work? I will close this issue for now. If you need further help please don't hesitate and re-open it.

best

It worked! Thanks so much!!