curvanato

local curvature quantification for anatomical data

Installation & Testing

To install the package locally, navigate to the package root and run:

python3 -m pip install curvanato 

if you want to see some examples of different things the package can do, clone the source package and investigate the contents of the tests directory.

Usage

import ants
import antspynet
import antspyt1w
import curvanato
import re
import os  # For checking file existence
import pandas as pd
import numpy as np
os.environ["ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS"] = "32"
ctype='fs'
tcaudR=curvanato.load_labeled_caudate( option='hmt', binarize=False, label=[2,4,6] )
caudseg=curvanato.load_labeled_caudate( option=ctype )
# this step is important - fs caudate segmentations look pretty terrible in comparison to what i am used to ....
caudseg=ants.threshold_image( caudseg, 50, 50 ).resample_image( [0.5,0.5,0.5], interp_type=0 ).threshold_image(0.5,1)
fn='/tmp/cc_example.nii.gz'
vlab=None
gr=0
subd=0
ccfn = [
        re.sub( ".nii.gz", "_"+ctype+"Rkappa.nii.gz" , fn ), 
        re.sub( ".nii.gz", "_"+ctype+"R.nii.gz" , fn ),
        re.sub( ".nii.gz", "_"+ctype+"Rthk.nii.gz" , fn ),
        re.sub( ".nii.gz", "_"+ctype+"Rkappa.csv" , fn ),
        re.sub( ".nii.gz", "_"+ctype+"Rkappa.png" , fn ),
        re.sub( ".nii.gz", "_"+ctype+"Rthk.png" , fn ) ]
pcaud=[3,4]
plabs=[4]
mytl=1
xx = curvanato.t1w_caudcurv(  caudseg, target_label=mytl, ventricle_label=vlab, 
        prior_labels=pcaud, prior_target_label=plabs, subdivide=subd, grid=gr,
        priorparcellation=tcaudR,  plot=True, smoothing=0.5,
        verbose=True )
ants.plot( xx[0], xx[1], crop=True, axis=2, nslices=21, ncol=7, filename=ccfn[4] )
ants.plot( xx[0], xx[2], crop=True, axis=2, nslices=21, ncol=7, filename=ccfn[5] )
for j in range(3):
    ants.image_write( xx[j], ccfn[j] )
xx[3].to_csv( ccfn[3] )

Example data

this package has been tested on ANTPD data from openneuro.

could also try data here which included repeated T1w acquisitions on same subjects but with different parameters. however, last time i tried this, the link was not working.

rm -r -f build/ curvanato.egg-info/ dist/
python3 -m  build .
python3 -m pip install --upgrade twine
python3 -m twine upload --repository curvanato dist/*