After all processing has been completed, the designated output directory for the
qap_anatomical_spatial.py
workflow will contain a set of pdf files that
contain the relevant reports for the set of scans undergoing quality assessment.
The set of output pdfs includes one pdf file per input scan in the scan directory,
e.g.: qap_anatomical_spatial_sub-01.pdf
, which contains the T1 slice
mosaic and QC metrics for that scan. There will also be a group report pdf in the
main output directory, e.g.: qap_anatomical_spatial_group.pdf
, that contains
summary metrics for the entire set of scans.
This plot in the report for the scan being assessed, e.g.:
Anatomical reoriented, subject sub-01 (session_1_anat_1)
is the rendering of the axial slices from the 3D stack created by the workflow. This image can be used to eyeball the quality of the overall signal in the anatomical scan, as it will be obvious if there were any problem areas where there was signal dropout resulting from a bad shim or other sources of signal distortion.
The metrics displayed in the Summary Report, e.g.: QC measures (subject sub-01_session_1)
were computed using the qap_anatomical_spatial.py
workflow and have been
displayed as violin plots. The stars in these plots denote where the score for the scans for this
participant fall in the distribution of all scores for scans that were included as inputs to the
anatomical-spatial workflow.
If there are several scans per session for this individual, then the stars will be displayed adjacent
to each other in the violin plot.
The metrics computed are as follows:
All metrics are described in more detail in the Taxonomy of QA Measures section of the QAP documentation. Please refer to the QAP website for descriptions of these metrics.
The violin plots included in the group report, e.g.: qqap_anatomical_spatial_group.pdf
,
are a graphical representation of the columnar values in the qap_anatomical_spatial.csv
file
that was created in the main output directory for the workflow. The scores for each metric described above
were aggregated to create the distributions that were plotted in both the individual and group reports.
Hence, the violin plots in the individual scan reports and the group reports are identical, except that
the group reports do not contain any stars denoting individual scans. These group reports are intended
to provide the user a means of visually inspecting the overall quality of the spatial data for that group
of anatomical scans.