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Python script & library to read hippocampal volumes computed by Freesurfer & ASHS
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fphammerle/freesurfer-volume-reader
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Python script & library to read hippocampal subfield volumes computed byFreesurfer & ASHS
- Freesurferhttps://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
- ASHShttps://sites.google.com/site/hipposubfields/home
pip3 install --user freesurfer-volume-readerfreesurfer-volume-reader --help
Releases follow thesemantic versioningscheme.
export SUBJECTS_DIR=/my/freesurfer/subjectsfreesurfer-volume-readeror
freesurfer-volume-reader /my/freesurfer/subjectsfreesurfer-volume-reader /my/freesurfer/subjects /other/freesurfer/subjects
or
fromfreesurfer_volume_readerimportfreesurferforvolume_fileinfreesurfer.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())
export SUBJECTS_DIR=/my/ashs/subjectsfreesurfer-volume-reader --source-types ashsor
freesurfer-volume-reader --source-types ashs -- /my/ashs/subjectsfreesurfer-volume-reader --source-types ashs -- /my/ashs/subjects /other/ashs/subjects
or
fromfreesurfer_volume_readerimportashsforvolume_fileinashs.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())
fromfreesurfer_volume_readerimportashsforvolume_fileinashs.IntracranialVolumeFile.find('/my/ashs/subjects'):print(volume_file.subject)print(volume_file.read_volume_mm3())print(volume_file.read_volume_series())
freesurfer-volume-reader --source-types ashs freesurfer-hipposf -- /my/subjectsfreesurfer-volume-reader --source-types ashs freesurfer-hipposf -- /my/ashs/subjects /my/freesurfer/subjects /other/subjects
pip3 install --user pipenvgit clone https://github.com/fphammerle/freesurfer-volume-reader.gitcd freesurfer-volume-readerpipenv run pylint freesurfer_volume_readerpipenv run pytestAbout
Python script & library to read hippocampal volumes computed by Freesurfer & ASHS
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