Support for the hierarchical rule is missing

[chrisgorgo]

Execution failed: /opt/spm12/spm_BIDS_App.m
Error using fileread (line 22)
Could not open file /snapshot/data/sub-001/fmap/sub-001_dir-AP_epi.json. No such file or directory.
Error in fileread (line 22)
Error in parse_subject (line 326)
Error in spm_BIDS (line 122)
Error in spm (line 1210)
Error in spm_standalone (line 115)

The correct JSON file was in /snapshot/data/dir-AP_epi.json

More info at https://openneuro.org/datasets/ds001105/versions/00001?app=SPM&version=17&job=5a298a27fce2fd0001047fb6

[gllmflndn]

Thanks for the report. I fixed the bug in the SPM12 repository and will rebuild the Docker container shortly. When this is done, is there a way to restart the SPM analysis on OpenNeuro?

PS: On the OpenNeuro page, there is a link to OSF in the "References and Links": https://osf.io/x32te/ and from there a link back to OpenNeuro: https://openneuro.org/datasets/ds001105 but you get "You are not authorized to view this dataset" as only this one works: https://openneuro.org/datasets/ds001105/versions/00001

[chrisgorgo]

Thanks for fixing this! If you publish a new version of SPM App on GitHub I will be able to deploy it on OpenNeuro and we will be able to submit a new job.

[gllmflndn]

v0.0.10 has landed. Thanks!

[chrisgorgo]

I'm ready for deployment, but I need a text description of the '--config' input argument. Thoughts?

Best, Chris

On Tue, Jan 9, 2018 at 11:30 AM, Guillaume notifications@github.com wrote:

v0.0.10 https://hub.docker.com/r/bids/spm/tags/ has landed. Thanks!

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[chrisgorgo]

Also - should I enable group level?

[gllmflndn]

I have added an example of a task at the group level (computing a mean structural image) so you can enable it.

The '--config' input argument allows to specify the path to a MATLAB script that contains a description of the task to perform at the participant or group level. See examples with the configuration files pipeline_participant.m and pipeline_group.m that are used by default, when the '--config' argument is not specified.

[chrisgorgo]

Thanks!

Does the app require a different config file for participant and group stages?

On OpenNeuro we pass the same inputs (including config files) to all stages. Also user does not have influence on which stages are run (for example for SPM we will always run participant stage followed by group stage). Does this align with the current design of SPM App?

Best, Chris

On Wed, Jan 10, 2018 at 10:57 AM, Guillaume notifications@github.com wrote:

I have added an example of a task at the group level (computing a mean structural image) so you can enable it.

The '--config' input argument allows to specify the path to a MATLAB script that contains a description of the task to perform at the participant or group level. See examples with the configuration files pipeline_participant.m and pipeline_group.m that are used by default, when the '--config' argument is not specified.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/BIDS-Apps/SPM/issues/11#issuecomment-356645724, or mute the thread https://github.com/notifications/unsubscribe-auth/AAOkp10m4Lib2Xv2nJiRowqdODbsE52dks5tJN3ngaJpZM4Q6OIe .

[gllmflndn]

Yes, the way I thought about it is to have a different configuration file per level of analysis - it kind of makes sense given that analyses are always different. That said, a single user-specified configuration file could be written like this:

if strcmp(BIDS_App.level,'participant')
    % first level analysis
else
    % second level analysis
end

so this is not a limitation for OpenNeuro. I could also add the option for '--config' to point to a folder (instead of a single file) that would contain configuration files for each level of analysis, and would be picked up appropriately automatically by the App.

[chrisgorgo]

Uploading folders via a browser is a bit tricky so the solution with a single file and if statements would work better. Could you update the example so I could point to it in the app description on OpenNeuro? Thanks!

Best, Chris

On Jan 10, 2018 12:45 PM, "Guillaume" notifications@github.com wrote:

Yes, the way I thought about it is to have a different configuration file per level of analysis - it kind of makes sense given that analyses are always different. That said, a single user-specified configuration file could be written like this:

if strcmp(BIDS_App,'participant') % first level analysis else % second level analysis end

so this is not a limitation for OpenNeuro. I could also add the option for '--config' to point to a folder (instead of a single file) that would contain configuration files for each level of analysis, and would be picked up appropriately automatically by the App.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/BIDS-Apps/SPM/issues/11#issuecomment-356680259, or mute the thread https://github.com/notifications/unsubscribe-auth/AAOkp2P1gjJ_1PIUn-ltGOpWIiVytihOks5tJPdEgaJpZM4Q6OIe .

[gllmflndn]

I have added a paragraph about the configuration file in the README: https://github.com/BIDS-Apps/SPM#configuration-file

[chrisgorgo]

Thanks! I updated openneuro. You can take it for a spin if you want!

Best, Chris

On Thu, Jan 11, 2018 at 4:19 AM, Guillaume notifications@github.com wrote:

I have added a paragraph about the configuration file in the README: https://github.com/BIDS-Apps/SPM#configuration-file

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[gllmflndn]

Will do, thanks!