Documentation python package: confusing extensions

[Remi-Gau]

Documentation python package: confusing extensions

Documented in this issue: https://github.com/Remi-Gau/bids-app_rsHRF/issues/3

Several examples tend to a be a bit too specific and seem to imply that the files to be processed cannot have a .nii.gz extension.

For example:

docker run -ti --rm \
-v /path/to/input.nii:/input.nii:ro \
-v /path/to/mask.nii:/mask.nii \
-v /path/to/output/directory/results:/results \
bids/rshrf --input_file input.nii --atlas mask.nii --estimation canon2dd --output_dir results

Might probably be less confusing:

docker run -ti --rm \
-v /path/to/input:/input:ro \
-v /path/to/mask:/mask:ro \
-v /path/to/output/directory/results:/results \
bids/rshrf --input_file /input/input_file --atlas /mask/mask_file --estimation canon2dd --output_dir results

Or maybe it is just me, but it took me more than 30 minutes to track down the issue when trying to implement this.

[NigelCol]

Response to the issues documented in #3.

The instructions were updated taking the suggestions into account (https://github.com/BIDS-Apps/rsHRF/commit/e21fdfbd7ab98e932399a02e7926a78855ac18cc).

For a full overview of the instructions see : http://bids-apps.neuroimaging.io/rsHRF/

We also added additional sections for :

• the --bids_filter_file argument (added according to suggestions documented in #2).
• example use case of --bids_filter_file