Commandline --command option usage

[pbbaba]

Summary

I am trying to use --command populate-intended-for with the command line tool. Also I have created the heuristic.py file and added the following in it - POPULATE_INTENDED_FOR_OPTS = { 'matching_parameters': ['ImagingVolume', 'Shims'], 'criterion': 'Closest' }

Following is the final command when I am running heudiconv using command line - docker run --rm -it \
-v /Users/pbaba1/Documents/Data/human/dicom/triotim/amayer/macip_20637:/data:ro \ -v /Users/pbaba1/Documents/BIDS:/output \ nipy/heudiconv:latest \ -d "data/{subject}/{session}//.dcm" \ -s M87100217 \ --command populate-intended-for -ss Study20160325at134915 \ -f /output/code/heuristic.py \ -c dcm2niix -b \ -o /output

However, when I run this it gives me the following error - INFO: Running heudiconv version 1.0.0 latest 1.0.0 Traceback (most recent call last): File "/opt/miniconda-py39_4.12.0/bin/heudiconv", line 8, in sys.exit(main()) File "/src/heudiconv/heudiconv/cli/run.py", line 30, in main workflow(kwargs) File "/src/heudiconv/heudiconv/main.py", line 361, in workflow raise ValueError("'command' given but 'files' is None") ValueError: 'command' given but 'files' is None**

Is there something that I am missing? I could not find proper documentation that describes the --command option's correct usage. Please guide on this.

[yarikoptic]

https://github.com/nipy/heudiconv/pull/708 should fix it. Meanwhile - just provide some bogus paths in --files -- they will be ignored

[pbbaba]

But --files and -d options do not go together, and I need to provide -d option (--dicom_dir_template). Any solution on working without providing --files option?

[yarikoptic]

the easiest: wait for that PR to be merged, then you can try/use nipy/heudiconv:master instead of :latest (which is the released version)

[pbbaba]

This led to the following error when I run the nipy/heudiconv:master-

INFO: Running heudiconv version 1.0.0.post2+gaa4c785 latest 1.0.0 Traceback (most recent call last): File "/opt/miniconda-py39_4.12.0/bin/heudiconv", line 8, in sys.exit(main()) File "/src/heudiconv/heudiconv/cli/run.py", line 30, in main workflow(**kwargs) File "/src/heudiconv/heudiconv/main.py", line 373, in workflow assert dicom_dir_template is None AssertionError

[pbbaba]

Also this is not working with the command line tool. While using the command line for this tool, it gives me the same error that it gave while I posted this issue. Is there any way this can be implemented for the command line heudiconv?

[yarikoptic]

not sure what you mean by "command line" as a separate thing from something else since heudiconv is a command line tool and there is no other way (e.g. GUI). What did you mean?

In your invocation now just remove -d "data/{subject}/{session}//.dcm" since it is not relevant when you specify --command populate-intended-for -- it would operate on already converted data.

[pbbaba]

The installation method has local, docker and singularity type. I am using the local one using pip install heudiconv. Please refer to the documentation provided here: https://heudiconv.readthedocs.io/en/latest/installation.html I am using the first option i.e. Local

I am trying to get the conversion process and populate intended for run in one go. If I do not pass -d option how will it determine from where should it use the files for bids conversion.

[pbbaba]

Please refer to the below command that I am using: heudiconv \ --dicom_dir_template 'staging/xxx/xxxx/xxx/{subject}/{session}/*/*/*.dcm' \ --subjects A0000000 \ --ses v1 \ --heuristic BIDS_output/code/heuristic.py \ --converter dcm2niix \ --bids \ --command populate-intended-for \ --outdir BIDS_output

[yarikoptic]

ok. for clarity of terminology as I see it -- it is either "native" or "containerized" executions. All of them are "local" to me (e.g. if you used reproman and made it execute on some server -- it would have been not local. containers are all running locally). In all cases all invocations remain done in "command line".

• if you are doing full conversion, IntendedFor should be populated automatically if criteria set in heuristic are met. Do not specify any --command for conversion etc to happen
• --command populate-intended-for is intended to redo that particular step - population of IntendedFor e.g. if you modify the settings for it in the heuristic . Then it would just go through your BIDS_output directory and thus you should not specify --dicom_dir_template. FWIW I have merged https://github.com/nipy/heudiconv/pull/709 so in a few minutes whenever docker regenerates/pushes, if you pull that :master image -- you would get a new behavior that even if you specify that option -- it will proceed but issue a warning

[pbbaba]

Is it also applicable for python package heudiconv? (I am using pip install heudiconv and not docker pull nipy/hueudiconv:master and `docker run ...)

So if I used POPULATE_INTENDED_FOR_OPTS = { 'matching_parameters': ['ImagingVolume', 'Shims'], 'criterion': 'Closest' } in my heuristic.py file and run the above mentioned command without adding --command populate-intended-for, I should see that 'IntendedFor' flag is there in the .json files?

FYI the below screenshot shows how my heuristic.py file looks like.

[yarikoptic]

So if I used POPULATE_INTENDED_FOR_OPTS = { 'matching_parameters': ['ImagingVolume', 'Shims'], 'criterion': 'Closest' } in my heuristic.py file and run the above mentioned command without adding --command populate-intended-for, I should see that 'IntendedFor' flag is there in the .json files?

yes, if 'ImagingVolume', and 'Shims' matched ... if you don't see -- check sizes and Shimming in the .json files you get

[pbbaba]

Okay great! Thanks for your help, I will run this.

[github-actions[bot]]

:rocket: Issue was released in v1.0.1 :rocket:

[github-actions[bot]]

:rocket: Issue was released in v1.0.1 :rocket: