multi-channel/time-series medical image processing with antspyx
Project description
ANTsPyMM
processing utilities for timeseries/multichannel images - mostly neuroimaging
the outputs of these processes can be used for data inspection/cleaning/triage as well for interrogating hypotheses.
this package also keeps track of the latest preferred algorithm variations for production environments.
install by calling (within the source directory):
python setup.py install
or install via pip install antspymm
FIXME
what this will do
- FIXME
the processes FIXME
first time setup
import antspymm
antspymm.get_data()
NOTE: get_data
has a force_download
option to make sure the latest
package data is installed.
example processing
import os
os.environ["TF_NUM_INTEROP_THREADS"] = "8"
os.environ["TF_NUM_INTRAOP_THREADS"] = "8"
os.environ["ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS"] = "8"
import antspymm
import antspyt1w
import antspynet
import ants
img1 = ants.image_read( antspymm.get_data( "I1499279_Anon_20210819142214_5", target_extension=".nii.gz") )
img2 = ants.image_read( antspymm.get_data( "I1499337_Anon_20210819142214_6", target_extension=".nii.gz") )
dwp = antspymm.dewarp_imageset( [img1,img2] )
# now write out the mean and dewarped images for further processing, eg with dipy
to publish a release
python3 -m build
python -m twine upload -u username -p password dist/*
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