From 7d5b661d6dbd66dc29337cbad05203c827418acf Mon Sep 17 00:00:00 2001 From: duettwe <61516027+duettwe@users.noreply.github.com> Date: Wed, 15 Apr 2026 10:00:06 -0500 Subject: [PATCH 1/3] Document XnatRemoveResource and XnatResourceGather Add documentation for XnatRemoveResource and XnatResourceGather tools. I'm realizing now that these aren't even in the Xnat_tools directory AND they don't have the same --help output as the other tools. I'll need to correct those. --- docs/dax_command_line_tools.rst | 81 +++++++++++++++++++++++++++++++-- 1 file changed, 76 insertions(+), 5 deletions(-) diff --git a/docs/dax_command_line_tools.rst b/docs/dax_command_line_tools.rst index a5892c28..cf74e29e 100644 --- a/docs/dax_command_line_tools.rst +++ b/docs/dax_command_line_tools.rst @@ -21,6 +21,8 @@ Table of Contents 14. `Xnatsessionupdate <#xnatsessionupdate>`__ 15. `BIDSMapping <#bidsmapping>`__ 16. `XnatBOND <#xnatbond>`__ + 17. `XnatRemoveResource <#xnatremoveresource>`__ + 18. `XnatResourceGather <#xnatresourcegather>`__ List of the Tools ~~~~~~~~~~~~~~~~~ @@ -1129,11 +1131,80 @@ XnatBOND takes in a BIDS directory and detects the Key and Parameter Groups. Thi XnatBOND --bids_dir BIDS_DIR --modify_keyparam optional arguments: - -h, --help show this help message and exit - --bids_dir BIDS_DIR BIDS data directory. - -b BOND_DIR, --bond_dir BOND_DIR + -h, --help show this help message and exit + --bids_dir BIDS_DIR BIDS data directory. + -b BOND_DIR, --bond_dir BOND_DIR BOND data directory. - -m keyparam_edited keyparam_files new_keyparam_prefix, --modify_keyparam keyparam_edited keyparam_files new_keyparam_prefix + -m keyparam_edited keyparam_files new_keyparam_prefix, --modify_keyparam keyparam_edited keyparam_files new_keyparam_prefix Values to modify the keyparam in bids. - -o LOGFILE, --logfile LOGFILE + -o LOGFILE, --logfile LOGFILE Write the display/output in a file given to this OPTIONS. + +------------------ +XnatRemoveResource +------------------ + +XnatRemoveResoure will remove scan, scan resources, assessor, or assessor resources by PROJECT. + +:: + + # Tool to remove scan/resource data BY PROJECT + # - scan resources + # - entire scans + # - assessors given their status + # - entire assessor groups + # + # OPTIONS: + # --proj REQUIRED - Project you're wanting to remove data from + # [--scan] OPTIONAL - Scan type you want removed + # [--sc_resource] OPTIONAL - Resource of scan you want removed - MUST ALSO INCLUDE SCAN + # [--assess] OPTIONAL - Assessor type you want removed + # [--as_status] OPTIONAL - Status of assessor you want removed - MUST ALSO INCLUDE ASSESSOR + + Examples: + *Remove all T1 scans from given project + XnatRemoveResource --proj PROJECT --scan T1 + *Remove all slant_gpu_v1 assessors from the project + XnatRemoveResource --proj PROJECT --slant_gpu_v1 + *Remove all T1 NIFTI resources from given project + XnatRemoveResource --proj PROJECT --scan T1 --sc_resource NIFTI + *Remove all slant_gpu_v1 assessors with JOB_FAILED status from project + XnatRemoveResource --proj PROJECT --assess slant_gpu_v1 --as_status JOB_FAILED + +------------------ +XnatResourceGather +------------------ + +XnatResourceGather will display the inputs for all or given assessors for a given session + +:: + + ########################################################################## + # XnatResourceGather # + # # + # Developed by the MASI Lab Vanderbilt University, TN, USA. # + # If issues, please start a thread here: # + # https://groups.google.com/forum/#!forum/vuiis-cci # + # Usage: # + # Display all assessors inputs for a given session # + # Examples: # + # Check the help for examples by running --help # + ########################################################################## + + usage: XnatResourceGather [-h] --proj PROJECT --subj SUBJECT --sess SESSION [--assess ASSESSOR] + + What is the script doing : + *Generate a nested summary of the inputs for the assessor list + + Examples: + *Display list of all assessor inputs for given session: + XnatResourceGather --proj PROJECT --subj SUBJECT --sess SESSION + *Display list of slant_gpu_v1 input for given session + XnatResourceGather --proj PROJECT --subj SUBJECT --sess SESSION --assess slant_gpu_v1 + + optional arguments: + -h, --help show this help message and exit + --proj PROJECT Project to gather from + --subj SUBJECT Subject to gather from + --sess SESSION Session to gather from + --assess ASSESSOR Assessor selected for input list From 034bc145dd6e98e6670bf6bdb62f152485dff866 Mon Sep 17 00:00:00 2001 From: duettwe <61516027+duettwe@users.noreply.github.com> Date: Wed, 15 Apr 2026 10:01:31 -0500 Subject: [PATCH 2/3] Update usage line in dax_command_line_tools documentation Removed the help option from the usage line in the documentation. --- docs/dax_command_line_tools.rst | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/dax_command_line_tools.rst b/docs/dax_command_line_tools.rst index cf74e29e..1bf1ee3d 100644 --- a/docs/dax_command_line_tools.rst +++ b/docs/dax_command_line_tools.rst @@ -1191,7 +1191,7 @@ XnatResourceGather will display the inputs for all or given assessors for a give # Check the help for examples by running --help # ########################################################################## - usage: XnatResourceGather [-h] --proj PROJECT --subj SUBJECT --sess SESSION [--assess ASSESSOR] + usage: XnatResourceGather --proj PROJECT --subj SUBJECT --sess SESSION [--assess ASSESSOR] What is the script doing : *Generate a nested summary of the inputs for the assessor list @@ -1203,7 +1203,6 @@ XnatResourceGather will display the inputs for all or given assessors for a give XnatResourceGather --proj PROJECT --subj SUBJECT --sess SESSION --assess slant_gpu_v1 optional arguments: - -h, --help show this help message and exit --proj PROJECT Project to gather from --subj SUBJECT Subject to gather from --sess SESSION Session to gather from From 4660e680c9d15b94fc73d3524fd90b1c7ddd0534 Mon Sep 17 00:00:00 2001 From: duettwe <61516027+duettwe@users.noreply.github.com> Date: Fri, 17 Apr 2026 07:46:01 -0500 Subject: [PATCH 3/3] Update dax_command_line_tools.rst --- docs/dax_command_line_tools.rst | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/dax_command_line_tools.rst b/docs/dax_command_line_tools.rst index 1bf1ee3d..4ddb5f52 100644 --- a/docs/dax_command_line_tools.rst +++ b/docs/dax_command_line_tools.rst @@ -1187,8 +1187,6 @@ XnatResourceGather will display the inputs for all or given assessors for a give # https://groups.google.com/forum/#!forum/vuiis-cci # # Usage: # # Display all assessors inputs for a given session # - # Examples: # - # Check the help for examples by running --help # ########################################################################## usage: XnatResourceGather --proj PROJECT --subj SUBJECT --sess SESSION [--assess ASSESSOR]