https://github.com/andrewrosss/nii-info
Display NIfTI image information in a tabular format
https://github.com/andrewrosss/nii-info
cli nifti nifti-images tool
Last synced: 26 days ago
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Display NIfTI image information in a tabular format
- Host: GitHub
- URL: https://github.com/andrewrosss/nii-info
- Owner: andrewrosss
- License: mit
- Created: 2022-04-29T16:28:52.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2022-05-02T05:49:49.000Z (about 3 years ago)
- Last Synced: 2025-03-18T22:05:51.745Z (about 2 months ago)
- Topics: cli, nifti, nifti-images, tool
- Language: Python
- Homepage:
- Size: 30.3 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# nii-info
Display NIfTI image information in a tabular format
[](https://pypi.org/project/nii-info/)
## Installation
```bash
pip install nii-info
```
## Motivation
This package attempts to provide a quick and easy way to get a high-level overview of a collection of NIfTI images.
Often when dealing with a collection of NIfTI images the metadata describing those images is embeded across multiple files, specifically the nii images themselves, as well as potential JOSN sidecar files.
Of course, one can crack open a NIfTI file to inspect the header, or load a JSON sidecar into an editor to view its contents. However this quickly becomes tedious when one is dealing with many files and many fields of interest.
`nii-info` collects the values of fields of interest across a set of NIfTI files and aggregates them in a tablular format.
## Usage
`nii-info` exposes a CLI: `nii`
```text
$ nii --help
usage: nii [-h] [-o OUT_TSV] [-f FIELDS] [-v] [-D]
path [path ...]
Display NIfTI image information in a tabular format
...
positional arguments:
path nifti files or directories
containing nifti files,
directories are searched
recursively
optional arguments:
-h, --help show this help message and exit
-o OUT_TSV, --out-tsv OUT_TSV
file to write info to. (default:
stdout)
-f FIELDS, --fields FIELDS
Fields to include in the table.
-v, --version show program's version number and
exit
-D, --debug run program in debug mode
```
The `nii` CLI accepts a list of files and/or directories. Directories are searched recursively for `*.nii` and `*.nii.gz` files.
Simple usage might look something like:
```bash
nii /path/to/nii/file1.nii.gz /path/to/nii/file2.nii.gz /path/to/nii/dir/
```
## Modifying Fields/Columns
This application enables the user to modify which JSON sidecar & NIfTI header fields are included in the generated output via the `-f`/`--fields` option.
The `-f` option can be passed multiple times and uses a special syntax.
The argument for the `-f` option should be string of comma-separated values, where each value contains the "location", sidecar or nii header "key", and optional "label".
For example, to add the `FlipAngle` and `InversionTime` fields from the sidecars as well as the `datatype` and `descrip` fields from the NIfTI headers to the default set of outputs, the command could look something like:
```bash
nii \
-f 'sidecar:FlipAngle,sidecar:InversionTime' \
-f 'header:datatype,header:descrip:Header Description' \
/path/to/nii/dir/
```
In the above example, `sidecar:FlipAngle` tells the application to extract the `FlipAngle` field from each image's sidecar.
Additionally, `header:descrip:Header Description` tells the application to extract the `descrip` field from each image's NIfTI header and use the label `Header Descrption` as the column heading.
## Contributing
1. Have or install a recent version of `poetry` (version >= 1.1)
1. Fork the repo
1. Setup a virtual environment (however you prefer)
1. Run `poetry install`
1. Run `pre-commit install`
1. Add your changes (adding/updating tests is always nice too)
1. Commit your changes + push to your fork
1. Open a PR