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gdevenyi / NeuroAnsible

An ansible playbook to deploy a complete standalone neuroimaging workstation
GNU General Public License v3.0
22 stars 1 forks source link

dcm2bids binaries missing #35

Closed egarza closed 3 months ago

egarza commented 3 months ago

Ubuntu 24.04 LTS on a Windos Linux Subsystem Win11 PC.

This is the output of the installation.

egarza@CAMUS:~/NeuroAnsible$ ansible-playbook --ask-become-pass deploy.yml
BECOME password:

PLAY [workstations] ****************************************************************************************************

TASK [Gathering Facts] *************************************************************************************************
ok: [localhost]

TASK [mambaorg.micromamba : Check if micromamba already exists in /usr/local/bin/micromamba] ***************************
ok: [localhost]

TASK [mambaorg.micromamba : Install bzip2] *****************************************************************************
skipping: [localhost]

TASK [mambaorg.micromamba : Make temporary directory for micromamba] ***************************************************
skipping: [localhost]

TASK [mambaorg.micromamba : Install micromamba] ************************************************************************
skipping: [localhost]

TASK [mambaorg.micromamba : Copy micromamba to destination] ************************************************************
skipping: [localhost]

TASK [mambaorg.micromamba : Remove temporary directory] ****************************************************************
skipping: [localhost]

TASK [mambaorg.micromamba : Check if root_prefix is defined but doesn't exist] *****************************************
skipping: [localhost]

TASK [mambaorg.micromamba : Build first part of arguments] *************************************************************
skipping: [localhost]

TASK [mambaorg.micromamba : Build channel part of arguments] ***********************************************************
skipping: [localhost]

TASK [mambaorg.micromamba : Create a new conda environment] ************************************************************
skipping: [localhost]

TASK [mambaorg.micromamba : Create .condarc file] **********************************************************************
skipping: [localhost]

TASK [science : Create a scratch directory] ****************************************************************************
ok: [localhost]

TASK [science : Create quarantine paths] *******************************************************************************
ok: [localhost] => (item=/opt/quarantine/software)
ok: [localhost] => (item=/opt/quarantine/modulefiles)

TASK [science : lmod] **************************************************************************************************
ok: [localhost]

TASK [science : Fix environment variables for terminals/ssh in /etc/bash.bashrc] ***************************************
ok: [localhost]

TASK [science : Set MODULEPATH and QUARANTINE_PATH] ********************************************************************
ok: [localhost]

TASK [science : Copy module linker] ************************************************************************************
ok: [localhost]

TASK [science : Create AFNI directories] *******************************************************************************
ok: [localhost] => (item=/opt/quarantine/software/afni/2024-08-13/install)

TASK [science : Install AFNI dependencies] *****************************************************************************
ok: [localhost]

TASK [science : Link GSL library for AFNI to work] *********************************************************************
ok: [localhost]

TASK [science : Download AFNI installer] *******************************************************************************
ok: [localhost]

TASK [science : Run AFNI Installer] ************************************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Create freesurfer directories] *************************************************************************
ok: [localhost] => (item=/opt/quarantine/software/freesurfer/7.4.1)
ok: [localhost] => (item=/opt/quarantine/software/freesurfer/7.4.1/install)

TASK [science : install freesurfer 7.4.1] ******************************************************************************
skipping: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : install freesurfer license] ****************************************************************************
ok: [localhost]

TASK [science : Create ANTs directories] *******************************************************************************
ok: [localhost] => (item=/opt/quarantine/software/ANTs/2.5.2/install)

TASK [science : Install ANTs install dependencies] *********************************************************************
ok: [localhost]

TASK [science : Install ANTs] ******************************************************************************************
skipping: [localhost]

TASK [science : Move ANTs install files] *******************************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Create ANTs directories] *******************************************************************************
ok: [localhost] => (item=/opt/quarantine/software/fsl/6.0.7.11/install)
ok: [localhost] => (item=/opt/quarantine/software/fsl/6.0.7.11/src)

TASK [science : download fsl] ******************************************************************************************
ok: [localhost]

TASK [science : install fsl] *******************************************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : add apptainer ppa] *************************************************************************************
changed: [localhost] => (item=ppa:apptainer/ppa)

TASK [science : Install apptainer dependencies] ************************************************************************
ok: [localhost]

TASK [science : Create fmriprep directories] ***************************************************************************
ok: [localhost] => (item=/opt/quarantine/software/fmriprep/23.2.2/install)
ok: [localhost] => (item=/opt/quarantine/software/fmriprep/20.2.7/install)

TASK [science : Build fmriprep singularity container] ******************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Build fmriprep singularity container] ******************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Create fastsurfer directories] *************************************************************************
ok: [localhost] => (item=/opt/quarantine/software/fastsurfer/2.2.0/install)

TASK [science : Build fastsurfer singularity container] ****************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Create CPAC directory] *********************************************************************************
ok: [localhost] => (item=/opt/quarantine/software/cpac/0.5.1/install/bin)

TASK [science : Install pipx] ******************************************************************************************
ok: [localhost]

TASK [science : install cpac python wrapper] ***************************************************************************
changed: [localhost] => (item=cpac==0.5.1)

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Create civet directories] ******************************************************************************
ok: [localhost] => (item=/opt/quarantine/software/civet/2.1.1/install)
ok: [localhost] => (item=/opt/quarantine/software/civet/2.1.1/src)

TASK [science : Build civet singularity container] *********************************************************************
ok: [localhost]

TASK [science : Create a symbolic link] ********************************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Create directories] ************************************************************************************
ok: [localhost] => (item=/opt/quarantine/software/R/4.3)
ok: [localhost] => (item=/opt/quarantine/software/rstudio/2024.04.1-74/install)

TASK [science : copy R environment file] *******************************************************************************
ok: [localhost]

TASK [science : create R environment] **********************************************************************************
ok: [localhost]

TASK [science : copy condarc file] *************************************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Install mni_cortical_statistics (R)] *******************************************************************
ok: [localhost]

TASK [science : Install rstudio] ***************************************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Create directories] ************************************************************************************
ok: [localhost] => (item=/opt/quarantine/software/conda/2024-08-13)

TASK [science : copy python environment file] **************************************************************************
ok: [localhost]

TASK [science : create conda environment] ******************************************************************************
ok: [localhost]

TASK [science : copy condarc] ******************************************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Create minc directories] *******************************************************************************
ok: [localhost] => (item=/opt/quarantine/software/minc-toolkit-v2/1.9.18/install)
ok: [localhost] => (item=/opt/quarantine/software/minc-toolkit-v2/1.9.18/src)
ok: [localhost] => (item=/opt/quarantine/software/minc-stuffs/v0.1.25)
ok: [localhost] => (item=/opt/quarantine/software/minc2-simple/v2.2.30/build)

TASK [science : Install minc-toolkit-v2 build deps] ********************************************************************
ok: [localhost]

TASK [science : cpanm] *************************************************************************************************
[DEPRECATION WARNING]: The default value 'compatibility' for parameter 'mode' is being deprecated and it will be
replaced by 'new'. This feature will be removed from community.general in version 9.0.0. Deprecation warnings can be
disabled by setting deprecation_warnings=False in ansible.cfg.
ok: [localhost]

TASK [science : Download minc-toolkit-v2] ******************************************************************************
ok: [localhost] => (item=https://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.18-20220625-Ubuntu_20.04-x86_64.deb)
ok: [localhost] => (item=http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/beast-library-1.1.0-20121212.deb)
ok: [localhost] => (item=http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/bic-mni-models-0.1.1-20120421.deb)

TASK [science : Unpack minc-toolkit-v2 and delete unneeded ANTs tools] *************************************************
ok: [localhost]

TASK [science : Unpack beast-library-1.1] ******************************************************************************
ok: [localhost]

TASK [science : Unpack bic-mni-models] *********************************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Install pyminc (python)] *******************************************************************************
changed: [localhost]

TASK [science : clone minc-stuffs] *************************************************************************************
ok: [localhost]

TASK [science : get images in remote python src dir] *******************************************************************
ok: [localhost]

TASK [science : Install minc-stuffs (python)] **************************************************************************
ok: [localhost] => (item={'path': '/opt/quarantine/software/minc-stuffs/v0.1.25/src/python/compute_values_across_segmentation', 'mode': '0755', 'isdir': False, 'ischr': False, 'isblk': False, 'isreg': True, 'isfifo': False, 'islnk': False, 'issock': False, 'uid': 0, 'gid': 0, 'size': 1437, 'inode': 756578, 'dev': 2080, 'nlink': 1, 'atime': 1723571673.6323051, 'mtime': 1718648736.3161855, 'ctime': 1718648736.3161855, 'gr_name': 'root', 'pw_name': 'root', 'wusr': True, 'rusr': True, 'xusr': True, 'wgrp': False, 'rgrp': True, 'xgrp': True, 'woth': False, 'roth': True, 'xoth': True, 'isuid': False, 'isgid': False})
ok: [localhost] => (item={'path': '/opt/quarantine/software/minc-stuffs/v0.1.25/src/python/bayes_intensity_update', 'mode': '0755', 'isdir': False, 'ischr': False, 'isblk': False, 'isreg': True, 'isfifo': False, 'islnk': False, 'issock': False, 'uid': 0, 'gid': 0, 'size': 2666, 'inode': 756576, 'dev': 2080, 'nlink': 1, 'atime': 1723571673.8464904, 'mtime': 1718648736.3161855, 'ctime': 1718648736.3161855, 'gr_name': 'root', 'pw_name': 'root', 'wusr': True, 'rusr': True, 'xusr': True, 'wgrp': False, 'rgrp': True, 'xgrp': True, 'woth': False, 'roth': True, 'xoth': True, 'isuid': False, 'isgid': False})
ok: [localhost] => (item={'path': '/opt/quarantine/software/minc-stuffs/v0.1.25/src/python/voxel_vote', 'mode': '0755', 'isdir': False, 'ischr': False, 'isblk': False, 'isreg': True, 'isfifo': False, 'islnk': False, 'issock': False, 'uid': 0, 'gid': 0, 'size': 1810, 'inode': 756586, 'dev': 2080, 'nlink': 1, 'atime': 1723571674.0708747, 'mtime': 1718648736.3161855, 'ctime': 1718648736.3161855, 'gr_name': 'root', 'pw_name': 'root', 'wusr': True, 'rusr': True, 'xusr': True, 'wgrp': False, 'rgrp': True, 'xgrp': True, 'woth': False, 'roth': True, 'xoth': True, 'isuid': False, 'isgid': False})
ok: [localhost] => (item={'path': '/opt/quarantine/software/minc-stuffs/v0.1.25/src/python/volumes_from_labels_only', 'mode': '0755', 'isdir': False, 'ischr': False, 'isblk': False, 'isreg': True, 'isfifo': False, 'islnk': False, 'issock': False, 'uid': 0, 'gid': 0, 'size': 986, 'inode': 756585, 'dev': 2080, 'nlink': 1, 'atime': 1723571674.28506, 'mtime': 1718648736.3161855, 'ctime': 1718648736.3161855, 'gr_name': 'root', 'pw_name': 'root', 'wusr': True, 'rusr': True, 'xusr': True, 'wgrp': False, 'rgrp': True, 'xgrp': True, 'woth': False, 'roth': True, 'xoth': True, 'isuid': False, 'isgid': False})
ok: [localhost] => (item={'path': '/opt/quarantine/software/minc-stuffs/v0.1.25/src/python/measure_xcorr', 'mode': '0755', 'isdir': False, 'ischr': False, 'isblk': False, 'isreg': True, 'isfifo': False, 'islnk': False, 'issock': False, 'uid': 0, 'gid': 0, 'size': 1278, 'inode': 756579, 'dev': 2080, 'nlink': 1, 'atime': 1723571674.4890456, 'mtime': 1718648736.3161855, 'ctime': 1718648736.3161855, 'gr_name': 'root', 'pw_name': 'root', 'wusr': True, 'rusr': True, 'xusr': True, 'wgrp': False, 'rgrp': True, 'xgrp': True, 'woth': False, 'roth': True, 'xoth': True, 'isuid': False, 'isgid': False})
ok: [localhost] => (item={'path': '/opt/quarantine/software/minc-stuffs/v0.1.25/src/python/replace_label_with_nearest_valid_label', 'mode': '0755', 'isdir': False, 'ischr': False, 'isblk': False, 'isreg': True, 'isfifo': False, 'islnk': False, 'issock': False, 'uid': 0, 'gid': 0, 'size': 10443, 'inode': 756582, 'dev': 2080, 'nlink': 1, 'atime': 1723571674.7236295, 'mtime': 1718648736.3161855, 'ctime': 1718648736.3161855, 'gr_name': 'root', 'pw_name': 'root', 'wusr': True, 'rusr': True, 'xusr': True, 'wgrp': False, 'rgrp': True, 'xgrp': True, 'woth': False, 'roth': True, 'xoth': True, 'isuid': False, 'isgid': False})
ok: [localhost] => (item={'path': '/opt/quarantine/software/minc-stuffs/v0.1.25/src/python/rotational_minctracc.py', 'mode': '0755', 'isdir': False, 'ischr': False, 'isblk': False, 'isreg': True, 'isfifo': False, 'islnk': False, 'issock': False, 'uid': 0, 'gid': 0, 'size': 22350, 'inode': 756583, 'dev': 2080, 'nlink': 1, 'atime': 1723571674.9480138, 'mtime': 1718648736.3161855, 'ctime': 1718648736.3161855, 'gr_name': 'root', 'pw_name': 'root', 'wusr': True, 'rusr': True, 'xusr': True, 'wgrp': False, 'rgrp': True, 'xgrp': True, 'woth': False, 'roth': True, 'xoth': True, 'isuid': False, 'isgid': False})
ok: [localhost] => (item={'path': '/opt/quarantine/software/minc-stuffs/v0.1.25/src/python/compute_determinant.py', 'mode': '0755', 'isdir': False, 'ischr': False, 'isblk': False, 'isreg': True, 'isfifo': False, 'islnk': False, 'issock': False, 'uid': 0, 'gid': 0, 'size': 8424, 'inode': 756577, 'dev': 2080, 'nlink': 1, 'atime': 1723571675.1621988, 'mtime': 1718648736.3161855, 'ctime': 1718648736.3161855, 'gr_name': 'root', 'pw_name': 'root', 'wusr': True, 'rusr': True, 'xusr': True, 'wgrp': False, 'rgrp': True, 'xgrp': True, 'woth': False, 'roth': True, 'xoth': True, 'isuid': False, 'isgid': False})
ok: [localhost] => (item={'path': '/opt/quarantine/software/minc-stuffs/v0.1.25/src/python/minc_label_ops', 'mode': '0755', 'isdir': False, 'ischr': False, 'isblk': False, 'isreg': True, 'isfifo': False, 'islnk': False, 'issock': False, 'uid': 0, 'gid': 0, 'size': 6594, 'inode': 756580, 'dev': 2080, 'nlink': 1, 'atime': 1723571675.376384, 'mtime': 1718648736.3161855, 'ctime': 1718648736.3161855, 'gr_name': 'root', 'pw_name': 'root', 'wusr': True, 'rusr': True, 'xusr': True, 'wgrp': False, 'rgrp': True, 'xgrp': True, 'woth': False, 'roth': True, 'xoth': True, 'isuid': False, 'isgid': False})
ok: [localhost] => (item={'path': '/opt/quarantine/software/minc-stuffs/v0.1.25/src/python/smooth_vector', 'mode': '0755', 'isdir': False, 'ischr': False, 'isblk': False, 'isreg': True, 'isfifo': False, 'islnk': False, 'issock': False, 'uid': 0, 'gid': 0, 'size': 3958, 'inode': 756584, 'dev': 2080, 'nlink': 1, 'atime': 1723571675.590569, 'mtime': 1718648736.3161855, 'ctime': 1718648736.3161855, 'gr_name': 'root', 'pw_name': 'root', 'wusr': True, 'rusr': True, 'xusr': True, 'wgrp': False, 'rgrp': True, 'xgrp': True, 'woth': False, 'roth': True, 'xoth': True, 'isuid': False, 'isgid': False})
ok: [localhost] => (item={'path': '/opt/quarantine/software/minc-stuffs/v0.1.25/src/python/TFCE', 'mode': '0755', 'isdir': False, 'ischr': False, 'isblk': False, 'isreg': True, 'isfifo': False, 'islnk': False, 'issock': False, 'uid': 0, 'gid': 0, 'size': 4226, 'inode': 756575, 'dev': 2080, 'nlink': 1, 'atime': 1723571675.8047543, 'mtime': 1718648736.3161855, 'ctime': 1718648736.3161855, 'gr_name': 'root', 'pw_name': 'root', 'wusr': True, 'rusr': True, 'xusr': True, 'wgrp': False, 'rgrp': True, 'xgrp': True, 'woth': False, 'roth': True, 'xoth': True, 'isuid': False, 'isgid': False})
ok: [localhost] => (item={'path': '/opt/quarantine/software/minc-stuffs/v0.1.25/src/python/vtk_meshconvert.py', 'mode': '0755', 'isdir': False, 'ischr': False, 'isblk': False, 'isreg': True, 'isfifo': False, 'islnk': False, 'issock': False, 'uid': 0, 'gid': 0, 'size': 10032, 'inode': 756587, 'dev': 2080, 'nlink': 1, 'atime': 1723571676.0291386, 'mtime': 1718648736.3161855, 'ctime': 1718648736.3161855, 'gr_name': 'root', 'pw_name': 'root', 'wusr': True, 'rusr': True, 'xusr': True, 'wgrp': False, 'rgrp': True, 'xgrp': True, 'woth': False, 'roth': True, 'xoth': True, 'isuid': False, 'isgid': False})
ok: [localhost] => (item={'path': '/opt/quarantine/software/minc-stuffs/v0.1.25/src/python/pmincaverage', 'mode': '0755', 'isdir': False, 'ischr': False, 'isblk': False, 'isreg': True, 'isfifo': False, 'islnk': False, 'issock': False, 'uid': 0, 'gid': 0, 'size': 4895, 'inode': 756581, 'dev': 2080, 'nlink': 1, 'atime': 1723571676.2433236, 'mtime': 1718648736.3161855, 'ctime': 1718648736.3161855, 'gr_name': 'root', 'pw_name': 'root', 'wusr': True, 'rusr': True, 'xusr': True, 'wgrp': False, 'rgrp': True, 'xgrp': True, 'woth': False, 'roth': True, 'xoth': True, 'isuid': False, 'isgid': False})

TASK [science : Install minc-stuffs (perl)] ****************************************************************************
ok: [localhost]

TASK [science : clone minc2-simple] ************************************************************************************
ok: [localhost]

TASK [science : Install minc2-simple (python)] *************************************************************************
changed: [localhost]

TASK [science : Install minc2-simple (C)] ******************************************************************************
ok: [localhost]

TASK [science : Create CoBrALab directories] ***************************************************************************
ok: [localhost] => (item=/opt/quarantine/software/minc-toolkit-extras/20231023)
ok: [localhost] => (item=/opt/quarantine/software/iterativeN3/20230821)
ok: [localhost] => (item=/opt/quarantine/software/iterativeN4_multispectral/20210503)
ok: [localhost] => (item=/opt/quarantine/software/minc-bpipe-library/20230721)
ok: [localhost] => (item=/opt/quarantine/software/bpipe/0.9.12/install)

TASK [science : clone minc-toolkit-extras] *****************************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : clone iterativeN3] *************************************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : clone iterativeN4] *************************************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : clone minc-bpipe-library] ******************************************************************************
ok: [localhost]

TASK [science : Install bpipe dependency] ******************************************************************************
ok: [localhost]

TASK [science : install bpipe] *****************************************************************************************
skipping: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Create MRI Misc directories] ***************************************************************************
ok: [localhost] => (item=/opt/quarantine/software/itk-snap/4.2.0/install)
ok: [localhost] => (item=/opt/quarantine/software/3DSlicer/5.6.2/install)
ok: [localhost] => (item=/opt/quarantine/software/MRIcron/v1.2.20211006/install)
ok: [localhost] => (item=/opt/quarantine/software/MRIcroGL/v1.2.20220720/install)
ok: [localhost] => (item=/opt/quarantine/software/dcm2niix/v1.0.20240202/install)
ok: [localhost] => (item=/opt/quarantine/software/mi-brain/2020.04.09_r2e0ff5/install)
ok: [localhost] => (item=/opt/quarantine/software/mango/4.1/install)
ok: [localhost] => (item=/opt/quarantine/software/connectome-workbench/v1.5.0/install)
ok: [localhost] => (item=/opt/quarantine/software/dsi-studio/2023.12.06/install)
ok: [localhost] => (item=/opt/quarantine/software/c3d/1.4.0/install)
ok: [localhost] => (item=/opt/quarantine/software/dcm2bids/3.1.1/install)
ok: [localhost] => (item=/opt/quarantine/software/bpipe/0.9.12/install)

TASK [science : Install MRI misc dependencies and software] ************************************************************
ok: [localhost]

TASK [science : Install itk-snap] **************************************************************************************
skipping: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Install 3DSlicer] **************************************************************************************
skipping: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Install MRIcron] ***************************************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Install MRIcroGL] **************************************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Install dcm2niix] **************************************************************************************
skipping: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Install mi-brain] **************************************************************************************
skipping: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Install mango] *****************************************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Install connectome-workbench] **************************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Install dsi-studio] ************************************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Install mi-brain] **************************************************************************************
skipping: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Install dcm2bids] **************************************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Install bpipe] *****************************************************************************************
skipping: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Create directories] ************************************************************************************
ok: [localhost] => (item=/opt/quarantine/software/mrtrix3/3.0.4)
ok: [localhost] => (item=/opt/quarantine/software/mrtrix3tissue/5.2.9)

TASK [science : install mrtrix3] ***************************************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Install mtrix3tissue dependencies] *********************************************************************
ok: [localhost]

TASK [science : Git checkout mrtrix3tissue] ****************************************************************************
ok: [localhost]

TASK [science : Build mrtrix3tissue] ***********************************************************************************
ok: [localhost]

TASK [science : Install module] ****************************************************************************************
ok: [localhost]

TASK [science : Create nvidia module directories] **********************************************************************
changed: [localhost] => (item=/opt/quarantine/software/nvhpc/24.3/src)
ok: [localhost] => (item=/opt/quarantine/software/cuda/12.3.1/src)

TASK [science : Install nvidia development dependencies] ***************************************************************
ok: [localhost]

TASK [science : Download nvhpc] ****************************************************************************************
skipping: [localhost]

TASK [science : Run nvhpc Installer] ***********************************************************************************
ok: [localhost]

TASK [science : Cleanup downloaded nvhpc source] ***********************************************************************
changed: [localhost]

TASK [science : copy nvidia module activate] ***************************************************************************
ok: [localhost]

TASK [science : create resources directory] ****************************************************************************
ok: [localhost]

TASK [science : Install resources install dependencies] ****************************************************************
ok: [localhost]

TASK [science : Download and install minc MNI atlases] *****************************************************************
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://packages.bic.mni.mcgill.ca/mni-models/icbm152/mni_icbm152_lin_minc2.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://packages.bic.mni.mcgill.ca/mni-models/icbm152/mni_icbm152_nl_VI_minc2.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09a_minc2.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_asym_09a_minc2.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09b_minc2.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_asym_09b_minc2.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09c_minc2.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_asym_09c_minc2.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=https://packages.bic.mni.mcgill.ca/mni-models/icbm152/mni_icbm152_nlin_sym_09c_CerebrA_minc2.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://packages.bic.mni.mcgill.ca/mni-models/colin27/mni_colin27_1998_minc2.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://packages.bic.mni.mcgill.ca/mni-models/colin27/mni_colin27_2008_minc2.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://packages.bic.mni.mcgill.ca/mni-models/colin27/mni_colin27_2008_fuzzy_minc2.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://packages.bic.mni.mcgill.ca/mni-models/mni305/mni305_lin_minc2.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/~vfonov/nihpd/obj1/nihpd_sym_all_minc2.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/~vfonov/nihpd/obj1/nihpd_asym_all_minc2.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/~vfonov/nihpd/obj2/nihpd_obj2_asym_minc2.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://packages.bic.mni.mcgill.ca/mni-models/PD25/mni_PD25_20170213_minc2.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/users/llewis/CIVET_files/CIVET_2.0.tar.gz)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/users/llewis/CIVET_files/CIVET_1.12.tar.gz)

TASK [science : create directory for atlas files for mni_icbm152_lin_minc2] ********************************************
ok: [localhost]

TASK [science : Download atlas files for mni_icbm152_lin_minc2] ********************************************************
ok: [localhost]

TASK [science : create directory for atlas files for mni_icbm152_nl_VI_minc2] ******************************************
ok: [localhost]

TASK [science : Download atlas files for mni_icbm152_nl_VI_minc2] ******************************************************
skipping: [localhost]

TASK [science : create directory for atlas files for mni_icbm152_nlin_sym_09a_minc2] ***********************************
ok: [localhost]

TASK [science : Download atlas files for mni_icbm152_nlin_sym_09a_minc2] ***********************************************
skipping: [localhost]

TASK [science : create directory for atlas files for mni_icbm152_nlin_asym_09a_minc2] **********************************
ok: [localhost]

TASK [science : Download atlas files for mni_icbm152_nlin_asym_09a_minc2] **********************************************
skipping: [localhost]

TASK [science : create directory for atlas files for mni_icbm152_nlin_sym_09b_minc2] ***********************************
ok: [localhost]

TASK [science : Download atlas files for mni_icbm152_nlin_sym_09b_minc2] ***********************************************
skipping: [localhost]

TASK [science : create directory for atlas files for mni_icbm152_nlin_asym_09b_minc2] **********************************
ok: [localhost]

TASK [science : Download atlas files for mni_icbm152_nlin_asym_09b_minc2] **********************************************
skipping: [localhost]

TASK [science : create directory for atlas files for mni_icbm152_nlin_sym_09c_minc2] ***********************************
ok: [localhost]

TASK [science : Download atlas files for mni_icbm152_nlin_sym_09c_minc2] ***********************************************
skipping: [localhost]

TASK [science : create directory for atlas files for mni_icbm152_nlin_asym_09c_minc2] **********************************
ok: [localhost]

TASK [science : Download atlas files for mni_icbm152_nlin_asym_09c_minc2] **********************************************
skipping: [localhost]

TASK [science : create directory for atlas files for mni_icbm152_nlin_sym_09c_CerebrA_minc2] ***************************
ok: [localhost]

TASK [science : Download atlas files for mni_icbm152_nlin_sym_09c_CerebrA_minc2] ***************************************
ok: [localhost]

TASK [science : create directory for atlas files for mni_colin27_1998_minc2] *******************************************
ok: [localhost]

TASK [science : Download atlas files for mni_colin27_1998_minc2] *******************************************************
ok: [localhost]

TASK [science : create directory for atlas files for mni_colin27_2008_minc2] *******************************************
ok: [localhost]

TASK [science : Download atlas files for mni_colin27_2008_minc2] *******************************************************
ok: [localhost]

TASK [science : create directory for atlas files for mni_colin27_2008_fuzzy_minc2] *************************************
ok: [localhost]

TASK [science : Download atlas files for mni_colin27_2008_fuzzy_minc2] *************************************************
ok: [localhost]

TASK [science : create directory for atlas files for mni305_lin_minc2] *************************************************
ok: [localhost]

TASK [science : Download atlas files for mni305_lin_minc2] *************************************************************
skipping: [localhost]

TASK [science : create directory for atlas files for nihpd_sym_all_minc2] **********************************************
ok: [localhost]

TASK [science : Download atlas files for nihpd_sym_all_minc2] **********************************************************
ok: [localhost]

TASK [science : create directory for atlas files for nihpd_asym_all_minc2] *********************************************
ok: [localhost]

TASK [science : Download atlas files for nihpd_asym_all_minc2] *********************************************************
ok: [localhost]

TASK [science : create directory for atlas files for nihpd_obj2_asym_minc2] ********************************************
ok: [localhost]

TASK [science : Download atlas files for nihpd_obj2_asym_minc2] ********************************************************
ok: [localhost]

TASK [science : create directory for atlas files for mni_PD25_20170213_minc2] ******************************************
ok: [localhost]

TASK [science : Download atlas files for mni_PD25_20170213_minc2] ******************************************************
skipping: [localhost]

TASK [science : create directory for atlas files for CIVET_2.0.tar] ****************************************************
ok: [localhost]

TASK [science : Download atlas files for CIVET_2.0.tar] ****************************************************************
ok: [localhost]

TASK [science : create directory for atlas files for CIVET_1.12.tar] ***************************************************
ok: [localhost]

TASK [science : Download atlas files for CIVET_1.12.tar] ***************************************************************
ok: [localhost]

TASK [science : Download and install nifti MNI atlases] ****************************************************************
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://packages.bic.mni.mcgill.ca/mni-models/icbm152/mni_icbm152_lin_nifti.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://packages.bic.mni.mcgill.ca/mni-models/icbm152/mni_icbm152_nl_VI_nifti.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09a_nifti.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_asym_09a_nifti.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09b_nifti.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_asym_09b_nifti.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09c_nifti.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_asym_09c_nifti.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=https://packages.bic.mni.mcgill.ca/mni-models/icbm152/mni_icbm152_nlin_sym_09c_CerebrA_nifti.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://packages.bic.mni.mcgill.ca/mni-models/colin27/mni_colin27_1998_nifti.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://packages.bic.mni.mcgill.ca/mni-models/colin27/mni_colin27_2008_nifti.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://packages.bic.mni.mcgill.ca/mni-models/colin27/mni_colin27_2008_fuzzy_nifti.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://packages.bic.mni.mcgill.ca/mni-models/mni305/mni305_lin_nifti.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/~vfonov/nihpd/obj1/nihpd_sym_all_nifti.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/~vfonov/nihpd/obj1/nihpd_asym_all_nifti.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://www.bic.mni.mcgill.ca/~vfonov/nihpd/obj2/nihpd_obj2_asym_nifti.zip)
included: /home/egarza/NeuroAnsible/roles/science/tasks/resources-atlas-include.yml for localhost => (item=http://packages.bic.mni.mcgill.ca/mni-models/PD25/mni_PD25_20170213_nifti.zip)

TASK [science : create directory for atlas files for mni_icbm152_lin_nifti] ********************************************
ok: [localhost]

TASK [science : Download atlas files for mni_icbm152_lin_nifti] ********************************************************
skipping: [localhost]

TASK [science : create directory for atlas files for mni_icbm152_nl_VI_nifti] ******************************************
ok: [localhost]

TASK [science : Download atlas files for mni_icbm152_nl_VI_nifti] ******************************************************
skipping: [localhost]

TASK [science : create directory for atlas files for mni_icbm152_nlin_sym_09a_nifti] ***********************************
ok: [localhost]

TASK [science : Download atlas files for mni_icbm152_nlin_sym_09a_nifti] ***********************************************
skipping: [localhost]

TASK [science : create directory for atlas files for mni_icbm152_nlin_asym_09a_nifti] **********************************
ok: [localhost]

TASK [science : Download atlas files for mni_icbm152_nlin_asym_09a_nifti] **********************************************
skipping: [localhost]

TASK [science : create directory for atlas files for mni_icbm152_nlin_sym_09b_nifti] ***********************************
ok: [localhost]

TASK [science : Download atlas files for mni_icbm152_nlin_sym_09b_nifti] ***********************************************
skipping: [localhost]

TASK [science : create directory for atlas files for mni_icbm152_nlin_asym_09b_nifti] **********************************
ok: [localhost]

TASK [science : Download atlas files for mni_icbm152_nlin_asym_09b_nifti] **********************************************
skipping: [localhost]

TASK [science : create directory for atlas files for mni_icbm152_nlin_sym_09c_nifti] ***********************************
ok: [localhost]

TASK [science : Download atlas files for mni_icbm152_nlin_sym_09c_nifti] ***********************************************
skipping: [localhost]

TASK [science : create directory for atlas files for mni_icbm152_nlin_asym_09c_nifti] **********************************
ok: [localhost]

TASK [science : Download atlas files for mni_icbm152_nlin_asym_09c_nifti] **********************************************
skipping: [localhost]

TASK [science : create directory for atlas files for mni_icbm152_nlin_sym_09c_CerebrA_nifti] ***************************
ok: [localhost]

TASK [science : Download atlas files for mni_icbm152_nlin_sym_09c_CerebrA_nifti] ***************************************
ok: [localhost]

TASK [science : create directory for atlas files for mni_colin27_1998_nifti] *******************************************
ok: [localhost]

TASK [science : Download atlas files for mni_colin27_1998_nifti] *******************************************************
ok: [localhost]

TASK [science : create directory for atlas files for mni_colin27_2008_nifti] *******************************************
ok: [localhost]

TASK [science : Download atlas files for mni_colin27_2008_nifti] *******************************************************
ok: [localhost]

TASK [science : create directory for atlas files for mni_colin27_2008_fuzzy_nifti] *************************************
ok: [localhost]

TASK [science : Download atlas files for mni_colin27_2008_fuzzy_nifti] *************************************************
ok: [localhost]

TASK [science : create directory for atlas files for mni305_lin_nifti] *************************************************
ok: [localhost]

TASK [science : Download atlas files for mni305_lin_nifti] *************************************************************
skipping: [localhost]

TASK [science : create directory for atlas files for nihpd_sym_all_nifti] **********************************************
ok: [localhost]

TASK [science : Download atlas files for nihpd_sym_all_nifti] **********************************************************
ok: [localhost]

TASK [science : create directory for atlas files for nihpd_asym_all_nifti] *********************************************
ok: [localhost]

TASK [science : Download atlas files for nihpd_asym_all_nifti] *********************************************************
ok: [localhost]

TASK [science : create directory for atlas files for nihpd_obj2_asym_nifti] ********************************************
ok: [localhost]

TASK [science : Download atlas files for nihpd_obj2_asym_nifti] ********************************************************
ok: [localhost]

TASK [science : create directory for atlas files for mni_PD25_20170213_nifti] ******************************************
ok: [localhost]

TASK [science : Download atlas files for mni_PD25_20170213_nifti] ******************************************************
skipping: [localhost]

TASK [science : Download CoBrALab atlas labels] ************************************************************************
ok: [localhost]

TASK [science : create CoBrALab brains directory] **********************************************************************
ok: [localhost]

TASK [science : Download CoBrALab atlases] *****************************************************************************
skipping: [localhost] => (item=https://github.com/CoBrALab/atlases/releases/download/2.0/brains_t1.tar.bz2)
skipping: [localhost] => (item=https://github.com/CoBrALab/atlases/releases/download/2.0/brains_t2.tar.bz2)
skipping: [localhost] => (item=https://github.com/CoBrALab/atlases/releases/download/2.0/masks.tar.bz2)
skipping: [localhost]

PLAY RECAP *************************************************************************************************************
localhost                  : ok=207  changed=6    unreachable=0    failed=0    skipped=40   rescued=0    ignored=0
egarza@CAMUS:~$ module avail

--------------------------------------------- /opt/quarantine/modulefiles ----------------------------------------------
   3DSlicer/5.6.2                conda/2024-08-13            (D)    iterativeN3/20230821
   ANTs/2.5.2                    connectome-workbench/v1.5.0        iterativeN4_multispectral/20210503
   MRIcroGL/v1.2.20220720        cpac/0.5.1                         itk-snap/4.2.0
   MRIcron/v1.2.20211006         dcm2bids/3.1.1                     mango/4.1
   R/4.3                         dcm2niix/v1.0.20240202             mi-brain/2020.04.09_r2e0ff5
   afni/2024-06-17               dsi-studio/2023.12.06              minc-toolkit-extras/20231023
   afni/2024-08-13        (D)    fastsurfer/2.2.0                   minc-toolkit-v2/1.9.18
   bpipe/0.9.12                  fmriprep/20.2.7                    mrtrix3/3.0.4
   c3d/1.4.0                     fmriprep/23.2.2             (D)    mrtrix3tissue/5.2.9
   civet/2.1.1                   freesurfer/7.4.1                   rstudio/2024.04.1-74
   conda/2024-06-17              fsl/6.0.7.11

------------------------------- /opt/quarantine/software/nvhpc/24.3/install/modulefiles --------------------------------
   nvhpc-byo-compiler/24.3    nvhpc-hpcx-cuda12/24.3    nvhpc-nompi/24.3       nvhpc/24.3
   nvhpc-hpcx-cuda11/24.3     nvhpc-hpcx/24.3           nvhpc-openmpi3/24.3

------------------------------------------- /usr/share/lmod/lmod/modulefiles -------------------------------------------
   Core/lmod    Core/settarg (D)

I can load other modules, but dcm2bids seems not to load. The module is available.

When I load it:

egarza@CAMUS:~$ module load dcm2bids
egarza@CAMUS:~$ dbm2bids
dbm2bids: command not found
egarza@CAMUS:~$ dbm2bids_helper
dbm2bids_helper: command not found
egarza@CAMUS:~$

Others like DCM2NIIX work alright when loaded

egarza@CAMUS:~$ module load dcm2niix
egarza@CAMUS:~$ dcm2niix
Chris Rorden's dcm2niiX version v1.0.20240202  (JP2:OpenJPEG) (JP-LS:CharLS) GCC8.4.0 x86-64 (64-bit Linux)
usage: dcm2niix [options] <in_folder>
 Options :
  -1..-9 : gz compression level (1=fastest..9=smallest, default 6)
  -a : adjacent DICOMs (images from same series always in same folder) for faster conversion (n/y, default n)
  -b : BIDS sidecar (y/n/o [o=only: no NIfTI], default y)
   -ba : anonymize BIDS (y/n, default y)
  -c : comment stored in NIfTI aux_file (up to 24 characters e.g. '-c VIP', empty to anonymize e.g. 0020,4000 e.g. '-c ""')
  -d : directory search depth. Convert DICOMs in sub-folders of in_folder? (0..9, default 5)
  -e : export as NRRD (y) or MGH (o) or JSON/JNIfTI (j) or BJNIfTI (b) instead of NIfTI (y/n/o/j/b, default n)
  -f : filename (%a=antenna (coil) name, %b=basename, %c=comments, %d=description, %e=echo number, %f=folder name, %g=accession number, %i=ID of patient, %j=seriesInstanceUID, %k=studyInstanceUID, %m=manufacturer, %n=name of patient, %o=mediaObjectInstanceUID, %p=protocol, %r=instance number, %s=series number, %t=time, %u=acquisition number, %v=vendor, %x=study ID; %z=sequence name; default '%f_%p_%t_%s')
  -g : generate defaults file (y/n/o/i [o=only: reset and write defaults; i=ignore: reset defaults], default n)
  -h : show help
  -i : ignore derived, localizer and 2D images (y/n, default n)
  -l : losslessly scale 16-bit integers to use dynamic range (y/n/o [yes=scale, no=no, but uint16->int16, o=original], default o)
  -m : merge 2D slices from same series regardless of echo, exposure, etc. (n/y or 0/1/2, default 2) [no, yes, auto]
  -n : only convert this series CRC number - can be used up to 16 times (default convert all)
  -o : output directory (omit to save to input folder)
  -p : Philips precise float (not display) scaling (y/n, default y)
  -q : only search directory for DICOMs (y/l/n, default y) [y=show number of DICOMs found, l=additionally list DICOMs found, n=no]
  -r : rename instead of convert DICOMs (y/n, default n)
  -s : single file mode, do not convert other images in folder (y/n, default n)
  -u : up-to-date check
  -v : verbose (n/y or 0/1/2, default 0) [no, yes, logorrheic]
  -w : write behavior for name conflicts (0,1,2, default 2: 0=skip duplicates, 1=overwrite, 2=add suffix)
  -x : crop 3D acquisitions (y/n/i, default n, use 'i'gnore to neither crop nor rotate 3D acquistions)
  -z : gz compress images (y/o/i/n/3, default n) [y=pigz, o=optimal pigz, i=internal:zlib, n=no, 3=no,3D]
  --big-endian : byte order (y/n/o, default o) [y=big-end, n=little-end, o=optimal/native]
  --progress : Slicer format progress information (y/n, default n)
  --ignore_trigger_times : disregard values in 0018,1060 and 0020,9153
  --terse : omit filename post-fixes (can cause overwrites)
  --version : report version
  --xml : Slicer format features
 Defaults file : /home/egarza/.dcm2nii.ini
 Examples :
  dcm2niix /Users/chris/dir
  dcm2niix -c "my comment" /Users/chris/dir
  dcm2niix -o /users/cr/outdir/ -z y ~/dicomdir
  dcm2niix -f %p_%s -b y -ba n ~/dicomdir
  dcm2niix -f mystudy%s ~/dicomdir
  dcm2niix -o "~/dir with spaces/dir" ~/dicomdir

Thanks,

Eduardo

gdevenyi commented 3 months ago

Fixed.

Run ansible-playbook -t misc to avoid running through everything