We tried to run QC for BOLD data for all scan numbers of a session. So we deleted the --bolddata flag to use the default mode that includes all scans within a session.
While the commands were run, we don’t see any output in the session folder until we test it by specifying some scan numbers in the --bolddata flag (please see example below).
--bolddata='1,2' \
We are not sure if there is an alternative way to include all scan numbers in the session. Thanks in advance for any support you could provide!
No unfortunately run_qc does not support this at the moment. We have a plan to upgrade run_qc in the future, but there are some more pressing developments in the pipeline right now, so I cannot really give an eta.
Replace the batchfile with another one if what is specified above is not correct.
Also note that I changed the container version to latest which always make sense, since the latest container should be the best one there is. I also tweaked the scheduler parameters for your call, you do not really need the GPU node and that much memory for run_QC. By optimizing the scheduler parameter your jobs will be start running earlier.
Another solution here, and a better one than the proposed one is to pass sessions to run_qc through the --sessionsbatchfile parameter. This way run_qc should be able to run over all BOLDs. The thing is that QuNex cannot know which BOLDs a session has only from a list of sessions it needs additional info provided through the batch file.
Hi Jure, I suspect there is still a bug in the code that needs to be patched. We tried the following command (with batchfile parameter specified):
We are using v0.91.10 below for consistency with earlier commands in this same study.
The error is shown below (copied from /gpfs/project/fas/n3/Studies/ABCD/site21/processing/logs/comlogs/error_run_qc_NDARINVZ0TL0G08_baselineYear1Arm1_2022-02-08_11.48.0670377114.log).
# Generated by QuNex 0.91.10 on 2022-02-08_11.48.0670377114
#
---> Scene files found in:
/opt/qunex/qx_library/data/scenes/qc/template_bold_qc.wb.scene
/opt/qunex/qx_library/data/scenes/qc/template_gbc_bold_qc.wb.scene
/opt/qunex/qx_library/data/scenes/qc/template_pconn_bold_qc.wb.scene
/opt/qunex/qx_library/data/scenes/qc/template_scalar_bold_qc.wb.scene
---> Suffix not manually set. Setting default: 2022-02-08_11.47.0127710713
---> hcp_suffix flag not explicitly provided. Using defaults:
Note: BOLD input list not specified. Relying individual information files.
BOLD prefix not specified. Assuming no prefix
-- qunex.sh: Specified Command-Line Options - Start --
Study Folder: /gpfs/project/fas/n3/Studies/ABCD/site21
Session Folder: /gpfs/project/fas/n3/Studies/ABCD/site21/sessions
Sessions: NDARINVZ0TL0G08_baselineYear1Arm1
QC Modality: BOLD
QC Output Path: /gpfs/project/fas/n3/Studies/ABCD/site21/sessions/QC/BOLD
Custom QC requested: no
HCP suffix:
Session batch file requested: /gpfs/project/fas/n3/Studies/ABCD/site21/processing/batch_hcp.txt
BOLD runs requested: all
Omit default QC: no
QC Scene Template Folder: /opt/qunex/qx_library/data/scenes/qc
QC User-defined Scene:
Overwrite prior run: yes
Time stamp for logging: 2022-02-08_11.47.0127710713
Zip Scene File: yes
BOLD data input:
BOLD prefix:
BOLD suffix: _Atlas
Skip Initial Frames: 0
Compute SNR Only: no
-- qunex.sh: Specified Command-Line Options - End --
------------------------- Start of work --------------------------------
--- Note: Overwrite requested.
--- Generating BOLD QC scene here: /gpfs/project/fas/n3/Studies/ABCD/site21/sessions/QC/BOLD
--- Checking and generating output folders...
RunQCLogFolder: /gpfs/project/fas/n3/Studies/ABCD/site21/sessions/QC/BOLD/qclog
Output path: /gpfs/project/fas/n3/Studies/ABCD/site21/sessions/QC/BOLD
--> For NDARINVZ0TL0G08_baselineYear1Arm1 searching for BOLD tags in batch file /gpfs/project/fas/n3/Studies/ABCD/site21/processing/batch_hcp.txt ...
ERROR: BOLDS variable not set. Something went wrong for NDARINVZ0TL0G08_baselineYear1Arm1. Check your batch file inputs!
The command seems to be parsing batch_hcp.txt properly, but is failing at Relying individual information files. This really should read Relying session_hcp.txt individual information files. The code of run_qc.sh suggests that if the bolddata parameter is empty, it looks for ${SessAcqInfoFile} in individual session folders (line 561). However, SessAcqInfoFile is not defined until later during the main function in the script, hence the inability of run_qc to find the relevant information.
I think this needs to be a patch where the section on BOLDS="${SessAcqInfoFile}" is moved to after SessAcqInfoFile is defined in the script. If this looks right to you, I can outline the steps on the dev Trello.
Lisa, the issue you outlined at the end of your post was just one part of the problem :). Anyhow thanks for identifying this. The issues has been now fixed. I successfully ran: