A tool to convert structural segmentation outputs from FSL's FIRST and FAST tool to NIDM. It takes the output of the "simple1" container and workflow which provides the results of FSL-based structural segmentation and provides them in a .json format. The fslsegstats2nidm program them converts these to NIDM which it can also add to the NIDM of the BIDS data structure.
- Create a 'clean' environment
$ conda create -n my_env python=3
- Activate this environment
$ conda activate my_env
- Install 'click' (since it for some reason dosent install with the main setup)
$ pip install click
- Clone this repo
git clone https://github.com/ReproNim/fsl_seg_to_nidm.git
- Run the setup script
$ cd fsl_seg_to_nidm
$ python setup.py install
- Done!
You can get information about how to run this tool by executing:
$ fslsegstats2nidm --help
usage: fs;_seg_to_nidm.py [-h] (-d DATA_FILE | -f SEGFILE) -subjid SUBJID -o
OUTPUT_DIR [-j] [-add_de] [-n NIDM_FILE]
[-forcenidm]
This program will load in JSON output from FSL's FAST/FIRST
segmentation tool, augment the FSL anatomical region designations with common data element
anatomical designations, and save the statistics + region designations out as
NIDM serializations (i.e. TURTLE, JSON-LD RDF)
options:
-h, --help show this help message and exit
-d DATA_FILE, --data_file DATA_FILE
Path to FSL FIRST/FAST JSON data file
-f SEGFILE, --seg_file SEGFILE
Path or URL to a specific FSL JSONstats file. Note,
currently this is tested on ReproNim data
-subjid SUBJID, --subjid SUBJID
If a path to a URL or a stats fileis supplied via the
-f/--seg_file parameters then -subjid parameter must
be set withthe subject identifier to be used in the
NIDM files
-o OUTPUT_DIR, --output OUTPUT_DIR
Output filename with full path
-j, --jsonld If flag set then NIDM file will be written as JSONLD
instead of TURTLE
-add_de, --add_de If flag set then data element data dictionary will be
added to nidm file else it will written to aseparate
file as fsl_cde.ttl in the output directory (or same
directory as nidm file if -n paramemteris used.
-n NIDM_FILE, --nidm NIDM_FILE
Optional NIDM file to add segmentation data to.
-forcenidm, --forcenidm
If adding to NIDM file this parameter forces the data
to be added even if the participantdoesnt currently
exist in the NIDM file.