diff --git a/.circleci/config.yml b/.circleci/config.yml index 8e0d498..80344b9 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -54,7 +54,7 @@ jobs: mkdir -p ${HOME}/data/ datalad install -s ///openneuro/ds002799 ${HOME}/data/ds002799 cd ${HOME}/data/ds002799/derivatives/fmriprep - datalad get sub-30[27]/ses-*/func/*run-*MNI152NLin2009cAsym*preproc*bold* + datalad get -J 2 sub-30[27]/ses-*/func/*run-*MNI152NLin2009cAsym*preproc*bold* datalad unlock sub-30[27]/ses-*/func/*run-*MNI152NLin2009cAsym*preproc*bold* - save_cache: key: my_cache diff --git a/README.md b/README.md index aa490d7..114bc4d 100644 --- a/README.md +++ b/README.md @@ -35,10 +35,17 @@ This can be used also for other multivariate pattern analyses in the absence of eye-tracking data. Decoded gaze positions allow computing eye movements. -Some basic quality control and outliers detection is also performed. +Some basic quality control and outliers detection is also performed: + +- for each run ![](https://github.com/cpp-lln-lab/bidsMReye/blob/main/docs/source/images/sub-01_task-auditory_space-MNI152NLin6Asym_desc-bidsmreye_eyetrack.png) + +- at the group level + +![](https://github.com/cpp-lln-lab/bidsMReye/blob/main/docs/source/images/group_eyetrack.png) + For more information, see the [User Recommendations](https://deepmreye.slite.com/p/channel/MUgmvViEbaATSrqt3susLZ/notes/kKdOXmLqe). If you have other questions, please reach out to the developer team. @@ -56,7 +63,7 @@ of deepmreye on Apple M1 for example. docker build --tag cpplab/bidsmreye:latest --file docker/Dockerfile . ``` -#### Pull (work in progress) +#### Pull Pull the latest docker image: @@ -157,7 +164,8 @@ If your data is not in MNI space, bidsmreye will also register the data to MNI. ```bash bidsmreye --action prepare \ bids_dir \ - output_dir + output_dir \ + participant ``` ## Computing the eye movements @@ -170,7 +178,8 @@ This will also generate a quality control report of the decoded eye movements. ```bash bidsmreye --action generalize \ bids_dir \ - output_dir + output_dir \ + participant ``` ## Doing it all at once @@ -179,9 +188,17 @@ bidsmreye --action generalize \ ```bash bidsmreye --action all \ bids_dir \ - output_dir + output_dir \ + participant ``` +## Group level summary + +bidsmreye --action qc \ + bids_dir \ + output_dir \ + group + ## Demo Please look up the [documentation](https://bidsmreye.readthedocs.io/en/latest/demo.html) diff --git a/docs/source/images/group_eyetrack.png b/docs/source/images/group_eyetrack.png new file mode 100644 index 0000000..6b87697 Binary files /dev/null and b/docs/source/images/group_eyetrack.png differ