B0 threshold is not a valid integrer: DEFAULT

[sue192]

• What are you trying to do?
• If you've tried running this with BrainSpace code already, how did you do so and what went wrong?
• Please tell us about your computing environment:
• Other information
  I am trying to run -proc_dwi. The DTI data I obtained from the Philips 3T MRI scanner. I have a *.bval file consisting of b=0, b=1000. no phase image.
  When I run the docker command (v0.2.0)
  bids=/home/sue/micapipe/BIDS
  out=/home/sue/micapipe/output
  fs_lic=/home/sue/micapipe/FreeSurferLicense/license.txt
  tmp=/home/sue/micapipe/tmp
  sub=001
  docker run -d --name micapipe --rm
  -v ${bids}:/bids
  -v ${out}:/out
  -v ${fs_lic}:/opt/licence.txt
  micalab/micapipe:v0.2.3
  -bids /bids -out /out -fs_licence /opt/licence.txt -threads 10
  -sub $sub
  -proc_structural
  -proc_surf
  -freesurfer
  -post_structural
  -proc_dwi
  -SC
  -proc_func
  -mainScanStr task-rest_bold
  -NSR
  -noFIX
  -GD
  -QC_subj

I get the message [ERROR].... DWI string or path does not match the default:try to set it with -dwi_main .

I modified the code according to this suggestion as follows:
bids=/home/sue/micapipe/BIDS
out=/home/sue/micapipe/output
fs_lic=/home/sue/micapipe/FreeSurferLicense/license.txt
tmp=/home/sue/micapipe/tmp
sub=001
dwiDir=/home/sue/micapipe/BIDS/sub-001/dwi
docker run -d --name micapipe --rm
-v ${bids}:/bids
-v ${out}:/out
-v ${fs_lic}:/opt/licence.txt
micalab/micapipe:v0.2.3
-bids /bids -out /out -fs_licence /opt/licence.txt -threads 10
-sub $sub
-proc_structural
-proc_surf
-freesurfer
-post_structural
-proc_dwi -dwi_main ${dwiDir}/sub-001_dwi.nii.gz
-SC
-proc_func
-mainScanStr task-rest_bold
-NSR
-noFIX
-GD
-QC_subj
I get the message [ERROR].... B0 threshold is not a valid inegrer: DEFAULT
If I don't run proc_dwi and SC, it runs smoothly.

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

I am running on a server with Ubuntu 20.04

[i-Zaak]

Would this help? It did help me... #99