BIDS session organization ignored

[mnarayan]

According to the documentation a data configuration file is not needed if data is in BIDS.

 --data_config_file DATA_CONFIG_FILE
                        Yaml file containing the location of the data that is
                        to be processed. Can be generated from the CPAC gui.
                        This file is not necessary if the data in bids_dir is
                        organized according to the BIDS format. This enables
                        support for legacy data organization and cloud based
                        storage. A bids_dir must still be specified when using
                        this option, but its value will be ignored.

However, if a participant has sub-01/ses-1, sub-01/ses-2 this information is not carried through. Instead all outputs are tagged with the labels session_1. I'm guessing nothing short of providing a full configuration file can fix this for now.

[egarza]

I didn't have that problem and I have more than one session. I get an output for each subject and session: sub-001_ses-1, sub-001_ses-2, etc.

[mnarayan]

@egarza My sessions are named differently i.e. they might have letters and numbers like ses-tp1 rather than just ses-1 and ses-2 and this might be the issue. Some pipelines seem to be able to handle that.

[chrisgorgo]

Session labels that include letters and numbers are indeed valid in BIDS.

On Thu, Aug 31, 2017 at 9:13 AM, mnarayan notifications@github.com wrote:

@egarza https://github.com/egarza My sessions are named differently i.e. they might have letters and numbers like ses-tp1 rather than just ses-1 and ses-2 and this might be the issue. Some pipelines seem to be able to handle that.

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[mnarayan]

Relatedly, the output format for multiple sessions doesn't follow exactly follow BIDS either. Since the sessions are not nested within subject folders but rather sub-001_ses-1, sub-001_ses-2, ...

[ccraddock]

@mnarayan the output of CPAC is not currently BIDS compliant. This is in part due to the lack of a ratified BIDS spec that handles these outputs. We will test to make sure that the session information is preserved in the outputs. But the naming and structure of the outputs will take much longer to change.