Preparing data for dashQC_fmri

To run dashQC_fmri on your own preprocessed data from fmriprep or NIAK you need to first run the corresponding data converter module. The converter modules are python scripts that reorganize the output data from fmriprep or NIAK into the folder structure expected by dashQC_fmri. They also pregenerate some of the larger visual representations so you can later run the dashboard without any lag. This process can take some time but only has to be performed once per preprocessed dataset.

Note

Make sure that you have completed the installation of dashQC_fmri before you try to follow the steps in this section.

Preparing data from a fmriprep pipeline

Note

To generate the dashQC_fmri data for a fmriprep pipeline we currently need access to the unprocessed raw data folder on which fmriprep was run. Please make sure that this location is reachable before you run the converter.

Let’s assume the raw data folder that fmriprep was run on is located at /path/to/my/raw/data and the output directory of your successfully completed fmriprep pipeline is located at /path/to/my/fmriprep/output/. To generate your dashQC_fmri report at /path/to/my/dashQC_fmri/report you would then run

python -m dashQC_fmri.fmriprep_report /path/to/my/fmriprep/output/ /path/to/my/dashQC_fmri/report /path/to/my/raw/data

Once the process has completed, navigate to /path/to/my/dashQC_fmri/report e.g.:

cd /path/to/my/dashQC_fmri/report

find the index.html file and open it in a browser (e.g. on Unix):

sensible-browser index.html

This will open the dashQC_fmri dashboard you have just generated.

Preparing data from a niak pipeline

Let’s assume the output directory of your successfully completed NIAK pipeline is located at /path/to/my/niak/output/. To generate your dashQC_fmri report at /path/to/my/dashQC_fmri/report you would then run

python -m dashQC_fmri.niak_report /path/to/my/niak/output/ /path/to/my/dashQC_fmri/report

Once the process has completed, navigate to /path/to/my/dashQC_fmri/report e.g.:

cd /path/to/my/dashQC_fmri/report

find the index.html file and open it in a browser (e.g. on Unix):

sensible-browser index.html

This will open the dashQC_fmri dashboard you have just generated.