Python script & library to read hippocampal subfield volumescomputed by Freesurfer & ASHS
Project description
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
pip3 install --user freesurfer-volume-reader freesurfer-volume-reader --help
Releases follow the semantic versioning scheme.
Usage
Freesurfer
export SUBJECTS_DIR=/my/freesurfer/subjects freesurfer-volume-reader
or
freesurfer-volume-reader /my/freesurfer/subjects freesurfer-volume-reader /my/freesurfer/subjects /other/freesurfer/subjects
or
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
export SUBJECTS_DIR=/my/ashs/subjects freesurfer-volume-reader --source-types ashs
or
freesurfer-volume-reader --source-types ashs -- /my/ashs/subjects freesurfer-volume-reader --source-types ashs -- /my/ashs/subjects /other/ashs/subjects
or
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
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
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
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
Project details
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