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))
The measurements/reporting dHCP structural pipeline are distributed under the terms outlined in LICENSE.txt.
You can run the tool in a docker container. This will work on any version of any platform, is automated, and fairly simple. First, install docker:
https://docs.docker.com/engine/installation/
Pull the latest version of the QC image:
$ docker pull biomedia/dhcp-structural-pipeline-measures:latest
Then enter:
$ docker run --rm -t -v $PWD/data:/data \
-u $(id -u):$(id -g) \
biomedia/dhcp-structural-pipeline-measures:latest \
/data/participants.tsv --reporting
This will mount the subdirectory data of
your current directory as /data in the container, then execute the tool
on the output of dhcp-structural-pipeline in that directory.
The file participants.tsv should list the scans to process. For example:
participant_id gender birth_ga
subject1 Female 44.0
The directory containing the participants.tsv file should be in the standard
layout for the pipeline.
This script creates:
| File | Description |
|---|---|
derivatives/anat_group_measurements.csv |
CSV file listing all measurements |
If the --reporting flag is used, it also generates:
| File | Description |
|---|---|
derivatives/anat_group.pdf |
PDF that specifies the sessions included |
derivatives/anat_group_qc.pdf |
PDF report for all the sessions |
derivatives/sub-*/ses-*/anat/sub-*_ses-*_qc.pdf |
PDF report for each session |
In the top directory of structural-pipeline-measure, use git to
switch to the branch you want to build, and enter:
$ docker build -t biomedia/dhcp-structural-pipeline-measures:latest .
$ docker push biomedia/dhcp-structural-pipeline-measures:latest
If you want to work on the code of the pipeline, it can be more convenient to install locally to your machine. Only read on if you need to do a local install.
The measurement scripts do not require installation.
The reporting (optional) can be installed as follows:
$ pip install packages/structural_dhcp_svg2rlg-0.3 --user
$ pip install packages/structural_dhcp_rst2pdf-aquavitae --user
$ pip install packages/structural_dhcp_mriqc --user
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
Then run with (eg.):
$ ./pipeline.sh ~/vol/dhcp-derived-data/derived_02Jun2018/participants.tsv --reporting