QC report functionality not working

jsheunis / fMRwhy

Facilitating BIDS-compatible multi-echo fMRI analysis and quality control with SPM12 and Matlab

GNU Lesser General Public License v2.1

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QC report functionality not working #8

Closed jsheunis closed 2 years ago

jsheunis commented 3 years ago

The line in fmrwhy_bids_workflowQC to call the report generation function is commented out, because that functionality is not functioning yet. To be implemented...

jsheunis commented 3 years ago

@jesperr17

V1 functionality now added in c9e8af1

The line that was commented out is now added and functional, i.e. the reporting functionality should run when running the QC workflow.

To create the report separately, run:

settings_fn = 'path/to/settings/m-file';
sub = 'subject-number';
options = fmrwhy_settings_load(settings_fn);
fmrwhy_bids_qcSubReport(sub, options)

A new settings file for the openneuro depression dataset has been created, since the added functionality required changes to the settings template file.

jesperr17 commented 3 years ago

I was running the script and got the following error:

jsheunis commented 3 years ago

Hi Jesper. It looks like this is just a parameter in the updated settings file that needs to be set. See here

I mentioned in the previous post that a new settings file was created. This implies that your settings file has to be updated, or you can use the new one that I created.

The error you get seems to suggest that you're still using the previous settings file.

jsheunis commented 3 years ago

Note: as suggested by @jesperr17, this variable and similar ones (resolution of T1w or functional data) should ideally be derived from the dataset itself.