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
process:
-
resting state
-
neuromelanin mid-brain images
-
DWI
-
flair
-
voxel-based cortical thickness
into tabular and template-based voxel-wise format.
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
... i/o code here ...
tabPro, normPro = antspymm.mm(
t1,
hier,
nm_image_list = mynm,
rsf_image = rsf,
dw_image = dwi,
bvals = bval_fname,
bvecs = bvec_fname,
flair_image = flair,
do_tractography=False,
do_kk=False,
do_normalization=True,
verbose=True )
antspymm.write_mm( '/tmp/test_output', t1wide, tabPro, normPro )
to publish a release
python3 -m build
python -m twine upload -u username -p password dist/*
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