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
Install
pip3 install --user freesurfer-volume-reader
freesurfer-volume-reader --helpReleases follow the semantic versioning scheme.
Usage
Freesurfer
export SUBJECTS_DIR=/my/freesurfer/subjects
freesurfer-volume-readeror
freesurfer-volume-reader /my/freesurfer/subjects
freesurfer-volume-reader /my/freesurfer/subjects /other/freesurfer/subjectsor
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 ashsor
freesurfer-volume-reader --source-types ashs -- /my/ashs/subjects
freesurfer-volume-reader --source-types ashs -- /my/ashs/subjects /other/ashs/subjectsor
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/subjectsTests
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
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freesurfer-volume-reader-2.1.1.tar.gz
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