Identifies the ROIs overlapped with clusters from some input NIFTI volume file.
Requirements:
python v3.5+numpypandasnibabel
FSL v6.0+
Note:
- This script depends heavily on several of
FSL's binaries, and is therefore not executable on Windows platforms. Pythonenvironmental issues may arise. If so, try this:export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${FSLDIR}/fslpython/envs/fslpython/lib.
usage: nifti_roi.py [-h] [-i STATS.nii.gz] [-o OUTPUT.csv] [--atlas-num INT]
[-a ATLAS.nii.gz] [-info ATLAS.info.csv] [-t FLOAT]
[-d FLOAT] [--dump-atlases]
Finds NIFTI volume clusters and writes the overlapping ROIs to a CSV file.
This process can be performed using either one to two methods:
1. A NIFTI volume file is provided, along with an atlas number to determine which ROI the cluster overlaps (this requires the input NIFTI volume to be in MNI space).
2. A NIFTI volume file is provided, along with a separate atlas NIFTI volume and an enumrated CSV file, that contains the ROI intensity values as a number-ROI pair (this requires the input NIFTI volume to be in this atlas' space.)
For a list of available atlases, see the '--dump-atlases' option for details.
Note: enumrated CSV files must not contain Window's carriage returns.
optional arguments:
-h, --help show this help message and exit
Required arguments:
-i STATS.nii.gz, -in STATS.nii.gz, --input STATS.nii.gz
NIFTI image file.
-o OUTPUT.csv, -out OUTPUT.csv, --output OUTPUT.csv
Output spreadsheet name.
Atlasquery options:
--atlas-num INT Atlas number. See '--dump-atlases' for details.
Stand-alone atlas options:
-a ATLAS.nii.gz, -atlas ATLAS.nii.gz, --atlas ATLAS.nii.gz
NIFTI atlas file.
-info ATLAS.info.csv, --atlas-info ATLAS.info.csv
Atlas information file.
Optional arguments:
-t FLOAT, -thresh FLOAT, --thresh FLOAT
Cluster threshold. [default: 0.95]
-d FLOAT, -dist FLOAT, --distance FLOAT
Minimum distance between clusters. [default: 0]
--dump-atlases Prints available atlases and its corresponding atlas number.