This is an additional package that computes measurements and creates reports for the dHCP Structural Pipeline.
The measurements include:
- volumes
- cortical surface measurements (surface area, thickness, curvature, sulcal depth, gyrification index (GI) )
Antonios Makropoulos: more
The measurements/reporting dHCP structural pipeline are distributed under the terms outlined in LICENSE.txt
The measurements scripts do not require installation.
The reporting (optional) can be installed as follows:
- pip install packages/structural_dhcp_svg2rlg-0.3/
- pip install packages/structural_dhcp_rst2pdf-aquavitae/
- pip install packages/structural_dhcp_mriqc/
In order to run this pipeline, the dHCP structural pipeline commands/tools need to be included in the shell PATH by running:
- . [dHCP_structural_pipeline_path]/parameters/path.sh
The pipeline can be run with the following command:
- ./pipeline.sh [derivatives_dir] [dataset_csv] ( --reporting ) ( -t [num_threads] )
where:
| Argument | Type | Description |
|---|---|---|
| derivatives_dir | string | The derivatives directory created from the structural pipeline |
| dataset_csv | CSV file | This is a comma-delimited file (CSV) with the sessions to be included in the measurements/reporting. It includes one line for each subject session: [subjectID], [sessionID], [age] e.g. subject-1, session-1, 32 subject-1, session-2, 44 ... subject-N, session-1, 36 |
| num_threads | integer | Number of threads (CPU cores) used (default: 1) (Optional) |
| If specified (--reporting), the pipeline will also generate PDF reports for the subjects. |
Examples:
- ./pipeline.sh derivatives dataset.csv
- ./pipeline.sh derivatives dataset.csv --reporting
- ./pipeline.sh derivatives dataset.csv --reporting -t 8
The output of the pipeline is the following files:
| Output | Description |
|---|---|
| [derivatives_dir]/anat_group_measurements.csv | CSV file that contains all the measurements for the sessions included |
| [derivatives_dir]/anat_group.pdf | PDF that specifies the sessions included (if --reporting is specified) |
| [derivatives_dir]/anat_group_qc.pdf | PDF report for all the sessions (if --reporting is specified) |
| [derivatives_dir]/sub-*/ses-*/anat/sub-*_ses-*_qc.pdf | PDF report for each session (if --reporting is specified) |