Problem wrapping bash commands in datalad run

Hi DataLad Team,

Thanks for this amazing tool which I am just learning to use and appreciate!

The handbook is awesome, but I keep on getting problems when wrapping even very simple bash commands in a datalad run command (on an Ubuntu 20.04.3 installed server).

Here is an example of a docker run command for mriqc, but it also happens with a simple mkdir command for example, generating a similar error

/bin/sh: 1: docker run -it --rm -v /data/proj_discoverie/BIDS:/data:ro -v /data/proj_discoverie/derivatives/mriqc:/out poldracklab/mriqc:0.16.1 /data /out participant --participant_label KUL007 --verbose --verbose-reports --fd_thres 0.9: not found

Adding bash or /bin/bash before the command does not help either, so any suggestion for a solution would be appreciated!

Thanks very much in advance!

Best wishes,

Lukas

Please share the complete invocation of the actual datalad command - hard to tell from the above.
Note that for working with containers while adhering to the best practices toward reproducible research (YODA principles etc), ideally you should use datalad-container extension. You could find examples in the handbook or repronim/containers.

Also, with today’s release of DataLad 0.15.0, run has a dry-run mode that should help you compose such commands more easily.

Hi Yarik & Michael,

Thanks for the prompt response!
Here are a few examples of the entire datalad run commands, the first one with a custom script and the second one with mriqc run in a docker container on my system (not included in the dataset though).

I do not think the issue has anything to do with the container issue, as it fails for simple bash scripts too.

The dry-run option works great though!

Any idea how to solve this?

Thx,

Lukas

datalad run -m “run KUL_dcm2bids.sh on sub-KUL007” --input “sourcedata/sub-KUL007/DICOM” --output “BIDS/*” “KUL_dcm2bids.sh -d sourcedata/sub-KUL007/DICOM -p KUL007 -c study_config/sequences.txt -a -v”

datalad run -m “run mriqc on sub-KUL007” -i “rawdata/sub-KUL007/” -o “derivatives/mriqc/” “docker run -it --rm -v /data/proj_discoverie/BIDS:/data:ro -v /data/proj_discoverie/derivatives/mriqc:/out poldracklab/mriqc:0.16.1 /data /out participant --participant_label KUL007 --verbose --verbose-reports --fd_thres 0.9”

this one works just fine for me:

$> echo "echo 1" > KUL_dcm2bids.sh; chmod +x KUL_dcm2bids.sh; datalad save 
add(ok): KUL_dcm2bids.sh (file)                                                                           
save(ok): . (dataset)                                                                                     
action summary:                                                                                           
  add (ok: 1)
  save (ok: 1)

(git-annex)lena:/tmp/testds[master]git
$> PATH=.:$PATH datalad run -m “run KUL_dcm2bids.sh on sub-KUL007” --input “sourcedata/sub-KUL007/DICOM” --output “BIDS/*” “KUL_dcm2bids.sh -d sourcedata/sub-KUL007/DICOM -p KUL007 -c study_config/sequences.txt -a -v”
[INFO   ] == Command start (output follows) ===== 
1
[INFO   ] == Command exit (modification check follows) ===== 

so detail must be in what that command does?

Hi Yarik,

Many thanks, will check it out again!

The strange thing is that the exact same command runs perfectly fine when not wrapped in a datalad run command, and this also applies to fmriprep-docker, docker run, and even simple bash commands like mkdir (see error messages in my earlier message).

The only difference with your situation is that the KUL_dcm2bids.sh script is located outside of the superdataset (or any subdatasets) in my case, but is in my path, so that should not be the problem I guess?

Or do scripts need to be in the dataset itself for them to be run with datalad run?

Thanks in advance for clarifying this!

Best wishes,

Lukas

Interestingly, when trying to run the entire datalad run command again, I now get an error that is similar to what I get when I try to run the simple bash commands of fmriprep or mriqc commands wrapped in datalad run:

/bin/sh: 1: KUL_dcm2bids.sh -d sourcedata/sub-KUL005 -p KUL005 -c study_config/sequences.txt -v: not found

Any help would be appreciated!

Thanks,

Lukas

Can you share the script? Could you check what /bin/sh you would have there (bash? dash?)? Could you paste/share entire invocation and output?

Also what PATH envvar you would have - unlikely you have that script installed systemwide on every box.

But also it looks like datalad tries to pass that entire invocation as a command name, which is odd. That is why want to see denture invocation and version of datalad

1 Like

Hi Yarik,

Thanks a lot once again!

I have datalad version 0.14.7

Here is the script https://github.com/treanus/KUL_NeuroImaging_Tools/blob/master/KUL_dcm2bids.sh, but the problem does also apply to other commands including fmriprep and mriqc it seems.

/bin/sh is bash

PATH is /home/luna.kuleuven.be/u0027997/.local/bin:/home/luna.kuleuven.be/u0027997/gitkraken:/opt/weasis/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/opt/KUL_apps/KUL_FWT:/opt/KUL_apps/KUL_FWT:/opt/KUL_apps/KUL_VBG:/opt/KUL_apps/KUL_NeuroImaging_Tools:/opt/KUL_apps/dcm2niix/build/bin:/opt/KUL_apps/ANTs_installed/bin/:/opt/mrtrix3/bin:/opt/anaconda3/bin:/opt/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/puppetlabs/bin

The script is in a cloned github repo with path /opt/KUL_apps/KUL_NeuroImaging_Tools

Here is the entire invocation and output

u0027997@gbw-s-labgas01:/data/proj_discoverie$ datalad run -m “run KUL_dcm2bids.sh on sub-KUL005” --input “sourcedata/sub-KUL005/" --output "BIDS/sub-KUL005/” “KUL_dcm2bids.sh -d sourcedata/sub-KUL005 -p KUL005 -c study_config/sequences.txt -v” --dry-run
[INFO ] Making sure inputs are available (this may take some time)
[INFO ] == Command start (output follows) =====
/bin/sh: 1: KUL_dcm2bids.sh -d sourcedata/sub-KUL005 -p KUL005 -c study_config/sequences.txt -v: not found
[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: ‘‘KUL_dcm2bids.sh -d sourcedata/sub-KUL005 -p KUL005 -c study_config/sequences.txt -v’ --dry-run’ failed with exitcode 127 under /data/proj_discoverie

Thanks a ton!

Lukas

Having that --dry-run at the end, makes datalad assume you have that long thing the command and --dry-run to be is argument. Move --dry-run to be eg right after run

Strangely enough, this is what I get then

u0027997@gbw-s-labgas01:~$ datalad run --dry-run -m “run KUL_dcm2bids.sh on sub-KUL005” --input “sourcedata/sub-KUL005/" --output "BIDS/sub-KUL005/” “KUL_dcm2bids.sh -d sourcedata/sub-KUL005 -p KUL005 -c study_config/sequences.txt -v”
[ERROR ] unknown argument: --dry-run

Thanks!

Lukas

Missed that - it was added in 0.15.0 and you are using 0.14.7

Thanks Yarik!

How can I update/upgrade?

Not sure whether this will solve the problem though, as it does not originate from the --dry-run option?

Lukas

depends on how you installed. If we pippip install --upgrade datalad. if conda – just wait a bit (update ongoing) or conda uninstall datalad && pip install datalad

what if you run without --dry-run?

Thanks Yarik!

Upgrading datalad to 0.15.0 using pip worked fine, enabling the dry-run option.

When I run without dry-run now, I get an error about an outdated git-annex version

u0027997@gbw-s-labgas01:/data/proj_discoverie$ datalad run -m "run KUL_dcm2bids.sh on sub-KUL005" -i "sourcedata/sub-KUL005" -o "BIDS/*" "KUL_dcm2bids.sh sourcedata/sub-KUL005 -p KUL005 -c study_config/sequences.txt -v"

[INFO ] Making sure inputs are available (this may take some time)
[ERROR ] OutdatedExternalDependency(No working git-annex installation of version >= 8.20200309. Visit http://handbook.datalad.org/r.html?install for instructions on how to install DataLad and git-annex… You have version 8.20200226) (OutdatedExternalDependency)

How shall I upgrade this?

Does not seem to work using pip or sudo apt-get upgrade or update, nor git annex upgrade in the repo? I also adapted git config based on upgrades

git config annex.autoupgraderepository true

I tried the following then

u0027997@gbw-s-labgas01:~$ sudo apt-get install git-annex

Reading package lists… Done
Building dependency tree
Reading state information… Done
git-annex is already the newest version (8.20200226-1).
git-annex set to manually installed.
The following packages were automatically installed and are no longer required:

  • libllvm11 libpython2-stdlib linux-headers-5.4.0-80 linux-headers-5.4.0-80-generic linux-image-5.4.0-80-generic linux-modules-5.4.0-80-generic linux-modules-extra-5.4.0-80-generic python2 python2-minimal shim*
    Use ‘sudo apt autoremove’ to remove them.
    0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.

The output reads “git-annex set to manually installed”, not sure whether this is a problem for datalad or any other applications using git-annex?

As far as I understand it, the problem seems to be that the version of git-annex that is installed on my Ubuntu 20.04.3 system while installing datalad (probably just using sudo apt-get install datalad as per these instructions from the handbook, rather than using pip) is not the most recent version, and that apt-get fails to update to more recent versions?

Thanks again,

Lukas

Hi Yarik & Team,

A quick update about this.

Uninstalling datalad and git-annex and then installing using the datalad installer (using -m pip for datalad, and -m datalad/git-annex:tested) did the trick, resulting in up-to-date versions of both datalad and git-annex.

A new problem arose, however, when wrapping fmriprep-docker into a datalad run command.
fmriprep runs fine, but the datalad save at the end bumps into permission denied errors when trying to add the large output files (.nii.gz) to the git-annex repo. Permissions for the respective dirs look fine, and the outputdir derivatives/fmriprep was correctly specified in the -o option “derivatives/fmriprep/*”.

I have this problem with my previous installation when running fmriprep-docker as a standalone command, followed by datalad save. Running the datalad save command as sudo solved the issue, but sudo datalad does not work anymore now, probably because of pip installation.

Which installation methods would you recommend to get both the most recent versions of datalad and git-annex, while at the same time being able to solve the above issue using sudo? Or do you have another workaround for this issue?

Thanks again,

Lukas

You are on Linux, so why not to use singularity container, even if built from docker (IIRC with datalad-container if you container-add docker://... it will import it into singularity. Also note that we have already prepared singularity containers for all bids apps within https://github.com/ReproNim/containers/ which I have mentioned before.

PS never use sudo unless you really need to perform some admin tasks! now you need to do something like sudo chown -R $USER.$USER DATASET_PATH to bring it to hopefully sane state in terms of permissions.

Hi Yarik,

Thanks for the suggestion.

I am trying to set up a workflow for this dataset, so simply started over again.

For now, I want to get things up and running without containerizing, i.e. with datalad run rather than container-run. The problem below does not depend on this, because I get the same problem when running fmriprep-docker as a standalone command (which works fine) and then trying to datalad save.

Things work fine for mriqc, but for fmriprep, I keep on running into the same issue: fmriprep runs fine, but things go awry when datalad tries to save - see full error below.

I tried several options including creating my fmriprep output directory as a subdataset (and even datalad get after that) before running fmriprep (from the superdataset), not specifying it before and letting fmriprep create it, but in every scenario, I keep on getting the error that the large files cannot be added (to git-annex).

Any idea what the problem may be and how I could solve it?

Thanks a lot again!

Lukas

Here is my command (scenario where I did not create the fmriprep output dir as a subdataset before)

datalad run -m “run fmriprep on sub-KUL007” -i “BIDS/sub-KUL007/*” -o “fmriprep/*” “fmriprep-docker /data/proj_discoverie/BIDS/ data/proj_discoverie/ participant --participant-label KUL007 --fs-license-file /opt/KUL_apps/freesurfer/license.txt --fs-no-reconall --fd-spike-threshold 0.9 --dvars-spike-threshold 2 --verbose --output-spaces MNI152NLin2009cAsym:res-2 --ignore fieldmaps --use-syn-sdc”

Here is the error

CommandError: 'git -c diff.ignoreSubmodules=none annex add --json --json-error-messages -c annex.dotfiles=true -- data/proj_discoverie/fmriprep/.bidsignore     data/proj_discoverie/fmriprep/dataset_description.json data/proj_discoverie/fmriprep/logs/CITATION.bib data/proj_discoverie/fmriprep/logs/CITATION.html data/proj_discoverie/fmriprep/logs/CITATION.md data/proj_discoverie/fmriprep/logs/CITATION.tex data/proj_discoverie/fmriprep/sub-KUL007.html data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_desc-brain_mask.json data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_desc-brain_mask.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_desc-preproc_T1w.json data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_desc-preproc_T1w.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_dseg.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_label-CSF_probseg.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_label-GM_probseg.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_label-WM_probseg.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_space-MNI152NLin2009cAsym_res-2_desc-preproc_T1w.json data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_space-MNI152NLin2009cAsym_res-2_desc-preproc_T1w.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_space-MNI152NLin2009cAsym_res-2_dseg.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_space-MNI152NLin2009cAsym_res-2_label-CSF_probseg.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_space-MNI152NLin2009cAsym_res-2_label-GM_probseg.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_space-MNI152NLin2009cAsym_res-2_label-WM_probseg.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/figures/sub-KUL007_desc-about_T1w.html data/proj_discoverie/fmriprep/sub-KUL007/figures/sub-KUL007_desc-conform_T1w.html data/proj_discoverie/fmriprep/sub-KUL007/figures/sub-KUL007_desc-summary_T1w.html data/proj_discoverie/fmriprep/sub-KUL007/figures/sub-KUL007_dseg.svg data/proj_discoverie/fmriprep/sub-KUL007/figures/sub-KUL007_space-MNI152NLin2009cAsym_T1w.svg data/proj_discoverie/fmriprep/sub-KUL007/figures/sub-KUL007_task-MIST_run-1_desc-carpetplot_bold.svg data/proj_discoverie/fmriprep/sub-KUL007/figures/sub-KUL007_task-MIST_run-1_desc-compcorvar_bold.svg 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data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-1_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-2_desc-confounds_timeseries.json data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-2_desc-confounds_timeseries.tsv data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-2_from-T1w_to-scanner_mode-image_xfm.txt data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-2_from-scanner_to-T1w_mode-image_xfm.txt data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-2_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-2_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-2_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-2_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.json data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-2_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-3_desc-confounds_timeseries.json data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-3_desc-confounds_timeseries.tsv data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-3_from-T1w_to-scanner_mode-image_xfm.txt data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-3_from-scanner_to-T1w_mode-image_xfm.txt data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-3_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-3_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-3_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-3_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.json data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-3_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-4_desc-confounds_timeseries.json data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-4_desc-confounds_timeseries.tsv data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-4_from-T1w_to-scanner_mode-image_xfm.txt data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-4_from-scanner_to-T1w_mode-image_xfm.txt data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-4_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-4_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-4_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-4_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.json data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-4_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz data/proj_discoverie/fmriprep/sub-KUL007/log/20210922-093126_c6a614d7-fbc3-44c8-9f6f-8464660e3691/fmriprep.toml' failed with exitcode 1 under /data/proj_discoverie [info keys: stdout_json]
>  data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_desc-brain_mask.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_desc-preproc_T1w.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_dseg.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_label-CSF_probseg.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_label-GM_probseg.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_label-WM_probseg.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_space-MNI152NLin2009cAsym_res-2_desc-preproc_T1w.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_space-MNI152NLin2009cAsym_res-2_dseg.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_space-MNI152NLin2009cAsym_res-2_label-CSF_probseg.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_space-MNI152NLin2009cAsym_res-2_label-GM_probseg.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/anat/sub-KUL007_space-MNI152NLin2009cAsym_res-2_label-WM_probseg.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-1_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-1_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-1_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-2_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-2_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-2_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-3_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-3_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-3_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-4_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-4_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz: setFileMode: permission denied (Operation not permitted)
>   data/proj_discoverie/fmriprep/sub-KUL007/func/sub-KUL007_task-MIST_run-4_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz: setFileMode: permission denied (Operation not permitted)
add: 26 failed

so – check owner/permissions on those files and directories they are under?
I bet since you are using Docker (although you said that without containerizing, you are using fmriprep-docker which I guess uses docker) – they might be owed by root, and hence those errors. That is why I suggested to use singularity instead so it runs in your user namespace. not familiar with fmriprep-docker enough to advice on either it does proper UID/GID mapping etc. But again – check permissions first!

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