Week 9 Quiz - question 8

Courses ABCD ReproNim
1

Hi all,

I have been working on the week 9 quiz using the online jupyterhub.
But when I copy/paste the following command:

run_first_all containers-run -s datalad --explicit fsl -o data/sub-01/anat/sub-01_T1w.nii.gz --output derivatives/first/sub-01/ -i L_Hipp,R_Hipp -n data/sub-01/anat/sub-01_T1w.nii.gz --input derivatives/first/sub-01/none -m none

I get the following error: bash: run_first_all: command not found

The other commands did work and if I look at my directory with ls -a I get the following output:
. … data .datalad derivatives .git .gitattributes .gitmodules

In the .datalad folder is a config file:

[datalad “dataset”]
id = 8f4bbb49-2287-46fe-bc1e-b4a04308f842
[datalad “containers.fsl”]
image = .datalad/environments/fsl/image
cmdexec = singularity exec --cleanenv {img} {cmd}

and environments/fsl directory with image file.

This suggests that the previous command worked: datalad containers-add fsl --url https://osf.io/epnxs/download --call-fmt “singularity exec --cleanenv {img} {cmd}”

Do you have any idea what the problem could be?

Thanks.

Kind regards,
Helene Hopman

2

The code mentioned above (which is mentioned in Question) is scrambled and needs to be put in correct order for it to work.

None

  • datalad containers-run -n fsl --explicit --input data/sub-01/anat/sub-01_T1w.nii.gz --output derivatives/first/sub-01/ run_first_all -i data/sub-01/anat/sub-01_T1w.nii.gz -o derivatives/first/sub-01/none -m none -s L_Hipp,R_Hipp

Fast

  • datalad containers-run -n fsl --explicit --input data/sub-01/anat/sub-01_T1w.nii.gz --output derivatives/first/sub-01/ run_first_all -i data/sub-01/anat/sub-01_T1w.nii.gz -o derivatives/first/sub-01/fast -m fast -s L_Hipp,R_Hipp
3

Thanks. I feel a bit stupid, but if I run that command I get the following output/error:

jovyan@44373dc96dd5:~/week9_analysis$ datalad containers-run -n fsl --explicit --input data/sub-01/anat/sub-01_T1w.nii.gz --output derivatives/first/sub-01/ run_first_all -i data/sub-01/anat/sub-01_T1w.nii.gz -o derivatives/first/sub-01/none -m none -s L_Hipp,R_Hipp
[INFO ] Making sure inputs are available (this may take some time)
[INFO ] == Command start (output follows) =====
Error: cannot find image data/sub-01/anat/sub-01_T1w.nii.gz
[INFO ] == Command exit (modification check follows) =====
[INFO ] The command had a non-zero exit code. If this is expected, you can save the changes with ‘datalad save -d . -r -F .git/COMMIT_EDITMSG’
CommandError: ‘singularity exec --cleanenv .datalad/environments/fsl/image run_first_all -i data/sub-01/anat/sub-01_T1w.nii.gz -o derivatives/first/sub-01/none -m none -s L_Hipp,R_Hipp’ failed with exitcode 1 under /home/jovyan/week9_analysis

Should I expect the non-zero exit code and save the changes with ‘datalad save -d . -r -F .git/COMMIT_EDITMSG’ or is there another problem that I missed?

Best,
Helene

4

From the ‘note’ part in the question -
’ If this is the case, you may need to unlock data/sub-01/anat/sub-01_T1w.nii.gz via (datalad unlock data/sub-01/anat/sub-01_T1w.nii.gz). and add --explicit to the datalad command.’

You may need to run datalad unlock data/sub-01/anat/sub-01_T1w.nii.gz before the ‘fast’ and ‘none’ commands to solve this issue.