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
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
Release files for freesurfer-volume-reader 2.1.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| freesurfer-volume-reader-2.1.1.tar.gz | 303.8 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| freesurfer_volume_reader-2.1.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 311.7 kB
Release files / freesurfer-volume-reader-2.1.1.tar.gz
| Download URL | freesurfer-volume-reader-2.1.1.tar.gz |
|---|---|
| Size | 303.8 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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|
Release files / freesurfer_volume_reader-2.1.1-py3-none-any.whl
| Download URL | freesurfer_volume_reader-2.1.1-py3-none-any.whl |
|---|---|
| Size | 7.9 kB |
| Tags | Python 3 |
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SHA-256 checksum How to use checksums |
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twine/3.3.0 pkginfo/1.4.2 requests/2.25.1 setuptools/52.0.0 requests-toolbelt/0.9.1 tqdm/4.57.0 CPython/3.9.4
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