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fphammerle
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freesurfer-volume-reader
tükrözi: https://github.com/fphammerle/freesurfer-volume-reader
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Fa: 3013d8f97a
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Fabian Peter Hammerle 3013d8f97a read_hippocampal_volume_file_dataframe test: ignore order of rows & columns to fix tests failing with python3.5 5 éve
examples 6c7366a6cb rename column: `volume` -> `volume_mm^3` 5 éve
freesurfer_volume_reader 6c7366a6cb rename column: `volume` -> `volume_mm^3` 5 éve
tests 3013d8f97a read_hippocampal_volume_file_dataframe test: ignore order of rows & columns to fix tests failing with python3.5 5 éve
.pylintrc 07b02d4e5b pylint: disable missing-docstring 5 éve
.travis.yml c9ccc6214b travis-ci: enable python3.5 5 éve
Pipfile 658cd31d97 recursively search for freesurfer's hippocampus volume files; csv output 5 éve
Pipfile.lock 658cd31d97 recursively search for freesurfer's hippocampus volume files; csv output 5 éve
README.md cde1485785 readme: added travis-ci badge 5 éve
setup.py 3efeac7f85 setup.py: fixed repo url 5 éve

README.md

freesurfer-volume-reader

Build Status

Python script & library to read hippocampal subfield volumes computed by Freesurfer

https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

Install

pip3 install --user freesurfer-volume-reader
freesurfer-volume-reader --help

Usage

export SUBJECTS_DIR=/my/freesurfer/subjects
freesurfer-volume-reader

or

freesurfer-volume-reader /my/freesurfer/subjects

or

from freesurfer_volume_reader import find_hippocampal_volume_files, \
                                     read_hippocampal_volume_file_dataframe

for volume_file_path in find_hippocampal_volume_files('/my/freesurfer/subjects'):
    print(read_hippocampal_volume_file_dataframe(volume_file_path))

Tests

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