Fabian Peter Hammerle
4c5670b416
pipeline: disable pandas=1.* build for python3.6 as pandas v1.2.0 dropped support; disable python3.8-dev build to save CI time
|
3 years ago | |
|---|---|---|
| .github | 4 years ago | |
| examples | 4 years ago | |
| freesurfer_volume_reader | 4 years ago | |
| tests | 4 years ago | |
| .coveragerc | 5 years ago | |
| .gitignore | 4 years ago | |
| .pylintrc | 4 years ago | |
| .travis.yml | 3 years ago | |
| CHANGELOG.md | 4 years ago | |
| Pipfile | 3 years ago | |
| Pipfile.lock | 3 years ago | |
| README.rst | 5 years ago | |
| setup.py | 4 years ago |
README.rst
freesurfer-volume-reader
========================
.. image:: https://travis-ci.org/fphammerle/freesurfer-volume-reader.svg?branch=master
:target: https://travis-ci.org/fphammerle/freesurfer-volume-reader
.. image:: https://coveralls.io/repos/github/fphammerle/freesurfer-volume-reader/badge.svg?branch=master
:target: https://coveralls.io/github/fphammerle/freesurfer-volume-reader?branch=master
.. image:: https://img.shields.io/pypi/v/freesurfer-volume-reader.svg
:target: https://pypi.org/project/freesurfer-volume-reader/#history
.. image:: https://img.shields.io/pypi/pyversions/freesurfer-volume-reader.svg
:target: https://pypi.org/project/freesurfer-volume-reader/
.. image:: https://zenodo.org/badge/183625692.svg
:target: https://zenodo.org/badge/latestdoi/183625692
Python script & library to read hippocampal subfield volumes computed by
Freesurfer & ASHS
- Freesurfer
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
- ASHS https://sites.google.com/site/hipposubfields/home
Install
-------
.. code:: sh
pip3 install --user freesurfer-volume-reader
freesurfer-volume-reader --help
Releases follow the `semantic versioning `__
scheme.
Usage
-----
Freesurfer
~~~~~~~~~~
.. code:: sh
export SUBJECTS_DIR=/my/freesurfer/subjects
freesurfer-volume-reader
or
.. code:: sh
freesurfer-volume-reader /my/freesurfer/subjects
freesurfer-volume-reader /my/freesurfer/subjects /other/freesurfer/subjects
or
.. code:: python
from freesurfer_volume_reader import freesurfer
for volume_file in freesurfer.HippocampalSubfieldsVolumeFile.find('/my/freesurfer/subjects'):
print(volume_file.subject, volume_file.hemisphere, volume_file.analysis_id)
print(volume_file.read_volumes_mm3())
print(volume_file.read_volumes_dataframe())
ASHS
~~~~
.. code:: sh
export SUBJECTS_DIR=/my/ashs/subjects
freesurfer-volume-reader --source-types ashs
or
.. code:: sh
freesurfer-volume-reader --source-types ashs -- /my/ashs/subjects
freesurfer-volume-reader --source-types ashs -- /my/ashs/subjects /other/ashs/subjects
or
.. code:: python
from freesurfer_volume_reader import ashs
for volume_file in ashs.HippocampalSubfieldsVolumeFile.find('/my/ashs/subjects'):
print(volume_file.subject, volume_file.hemisphere, volume_file.correction)
print(volume_file.read_volumes_mm3())
print(volume_file.read_volumes_dataframe())
Intracranial Volume
^^^^^^^^^^^^^^^^^^^
.. code:: python
from freesurfer_volume_reader import ashs
for volume_file in ashs.IntracranialVolumeFile.find('/my/ashs/subjects'):
print(volume_file.subject)
print(volume_file.read_volume_mm3())
print(volume_file.read_volume_series())
Freesurfer & ASHS
~~~~~~~~~~~~~~~~~
.. code:: sh
freesurfer-volume-reader --source-types ashs freesurfer-hipposf -- /my/subjects
freesurfer-volume-reader --source-types ashs freesurfer-hipposf -- /my/ashs/subjects /my/freesurfer/subjects /other/subjects
Tests
-----
.. code:: sh
pip3 install --user pipenv
git clone https://github.com/fphammerle/freesurfer-volume-reader.git
cd freesurfer-volume-reader
pipenv run pylint freesurfer_volume_reader
pipenv run pytest
========================
.. image:: https://travis-ci.org/fphammerle/freesurfer-volume-reader.svg?branch=master
:target: https://travis-ci.org/fphammerle/freesurfer-volume-reader
.. image:: https://coveralls.io/repos/github/fphammerle/freesurfer-volume-reader/badge.svg?branch=master
:target: https://coveralls.io/github/fphammerle/freesurfer-volume-reader?branch=master
.. image:: https://img.shields.io/pypi/v/freesurfer-volume-reader.svg
:target: https://pypi.org/project/freesurfer-volume-reader/#history
.. image:: https://img.shields.io/pypi/pyversions/freesurfer-volume-reader.svg
:target: https://pypi.org/project/freesurfer-volume-reader/
.. image:: https://zenodo.org/badge/183625692.svg
:target: https://zenodo.org/badge/latestdoi/183625692
Python script & library to read hippocampal subfield volumes computed by
Freesurfer & ASHS
- Freesurfer
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
- ASHS https://sites.google.com/site/hipposubfields/home
Install
-------
.. code:: sh
pip3 install --user freesurfer-volume-reader
freesurfer-volume-reader --help
Releases follow the `semantic versioning `__
scheme.
Usage
-----
Freesurfer
~~~~~~~~~~
.. code:: sh
export SUBJECTS_DIR=/my/freesurfer/subjects
freesurfer-volume-reader
or
.. code:: sh
freesurfer-volume-reader /my/freesurfer/subjects
freesurfer-volume-reader /my/freesurfer/subjects /other/freesurfer/subjects
or
.. code:: python
from freesurfer_volume_reader import freesurfer
for volume_file in freesurfer.HippocampalSubfieldsVolumeFile.find('/my/freesurfer/subjects'):
print(volume_file.subject, volume_file.hemisphere, volume_file.analysis_id)
print(volume_file.read_volumes_mm3())
print(volume_file.read_volumes_dataframe())
ASHS
~~~~
.. code:: sh
export SUBJECTS_DIR=/my/ashs/subjects
freesurfer-volume-reader --source-types ashs
or
.. code:: sh
freesurfer-volume-reader --source-types ashs -- /my/ashs/subjects
freesurfer-volume-reader --source-types ashs -- /my/ashs/subjects /other/ashs/subjects
or
.. code:: python
from freesurfer_volume_reader import ashs
for volume_file in ashs.HippocampalSubfieldsVolumeFile.find('/my/ashs/subjects'):
print(volume_file.subject, volume_file.hemisphere, volume_file.correction)
print(volume_file.read_volumes_mm3())
print(volume_file.read_volumes_dataframe())
Intracranial Volume
^^^^^^^^^^^^^^^^^^^
.. code:: python
from freesurfer_volume_reader import ashs
for volume_file in ashs.IntracranialVolumeFile.find('/my/ashs/subjects'):
print(volume_file.subject)
print(volume_file.read_volume_mm3())
print(volume_file.read_volume_series())
Freesurfer & ASHS
~~~~~~~~~~~~~~~~~
.. code:: sh
freesurfer-volume-reader --source-types ashs freesurfer-hipposf -- /my/subjects
freesurfer-volume-reader --source-types ashs freesurfer-hipposf -- /my/ashs/subjects /my/freesurfer/subjects /other/subjects
Tests
-----
.. code:: sh
pip3 install --user pipenv
git clone https://github.com/fphammerle/freesurfer-volume-reader.git
cd freesurfer-volume-reader
pipenv run pylint freesurfer_volume_reader
pipenv run pytest