This is an additional package that computes measurements and creates reports for the dHCP Structural Pipeline.
The measurements include:
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:
In order to run this pipeline, the dHCP structural pipeline commands/tools need to be included in the shell PATH by running:
The pipeline can be run with the following command:
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:
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) |