freesurfer-volume-reader's Introduction

freesurfer-volume-reader

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

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

freesurfer-volume-reader /my/freesurfer/subjects
freesurfer-volume-reader /my/freesurfer/subjects /other/freesurfer/subjects

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

freesurfer-volume-reader --source-types ashs -- /my/ashs/subjects
freesurfer-volume-reader --source-types ashs -- /my/ashs/subjects /other/ashs/subjects

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

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freesurfer-volume-reader's Issues

mybinder.org fails to open example notebook

https://mybinder.org/v2/gh/fphammerle/freesurfer-volume-reader/master

ERROR: Complete output from command python setup.py egg_info:
ERROR: Traceback (most recent call last):
  File "", line 1, in
  File "/tmp/pip-req-build-43n3oihg/setup.py", line 5, in
    import freesurfer_volume_reader
  File "/tmp/pip-req-build-43n3oihg/freesurfer_volume_reader/init.py", l23, in
    import pandas
ModuleNotFoundError: No module named 'pandas'

Add Test Coverage Badge

Add ASHS example

Semantic Versioning

https://semver.org/

Examples: Replace dummy test data with real measurements to improve plots

Read Freesurfer's aseg.stats

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/VolumetricGroupAnalysis

Fail gracefully when no volume file was found

Traceback (most recent call last):
File ".../bin/freesurfer-volume-reader", line 11, in
load_entry_point('freesurfer-volume-reader', 'console_scripts', 'freesurfer-volume-reader')()
File ".../freesurfer_volume_reader/main.py", line 59, in main
united_volume_frame = pandas.concat(volume_frames, ignore_index=True, sort=False)
File ".../lib/python3.6/site-packages/pandas/core/reshape/concat.py", line 228, in concat
copy=copy, sort=sort)
File ".../lib/python3.6/site-packages/pandas/core/reshape/concat.py", line 262, in init
raise ValueError('No objects to concatenate')
ValueError: No objects to concatenate

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