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.