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surface_processing_v3.4.py
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surface_processing_v3.4.py
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#!/usr/bin/env python3
#v3.4 - "--all_young" flag added to process fetuses younger than 28.5 GA
#surface extraction after segmentation_to31_final.nii created
'''
TO DO:
- use Tafoya's flag option for extraction WO subsample
'''
import os
import sys
import math
import argparse
import numpy as np
parser = argparse.ArgumentParser()
parser.add_argument('--input_fol',
nargs='?',
required=True,
help='path to the data directory')
parser.add_argument('--extraction',
dest='extrac',
action='store_true',
help='creates minc files, performs surface extract singularity, and transforms input objects with the corresponding .xfm transform')
parser.add_argument('--all_young',
dest='all_young',
action='store_true',
help='creates minc files, performs surface extract singularity, and transforms input objects with the corresponding .xfm transform')
parser.add_argument('--from_registration',
dest='reg__',
action='store_true',
help='function to register scan files to 28-31 GW templates')
parser.add_argument('--registration',
dest='surf_reg',
action='store_true',
help='function to register scan files to 28-31 GW templates')
parser.add_argument('--resample',
dest='resampling',
action='store_true',
help='sphere resampling and creating objects with transfometrics for surface extraction')
parser.add_argument('--surface_measures',
dest='surf_meas',
action='store_true',
help='calculates sulcal depth, surface area, mean curvature')
parser.add_argument('--volume_measures',
dest='vol_meas',
action='store_true',
help='volume measures stored in txt file')
parser.add_argument('--gyrification_index',
dest='GI',
action='store_true',
help='calculates and stores the gyrification index values in txt file')
parser.add_argument('--all',
dest='all',
action='store_true',
help='does all steps')
#surface extraction
def extraction_woSubsample():
os.system('nii2mnc '+input_fol+'/recon_segmentation/segmentation_to31_final.nii '+input_fol+'/temp/segmentation_to31_final.mnc;')
os.system('mincmath -clobber -eq -const 160 '+input_fol+'/temp/segmentation_to31_final.mnc '+input_fol+'/temp/inner_left.mnc;'
'mincmath -clobber -eq -const 161 '+input_fol+'/temp/segmentation_to31_final.mnc '+input_fol+'/temp/inner_right.mnc;')
os.system('singularity exec docker://fnndsc/pl-fetal-cp-surface-extract extract_cp --adapt_object_mesh 0,100,0,0 --mincmorph-iterations 1 '+input_fol+'/temp/ '+input_fol+'/temp/;')
os.system('adapt_object_mesh '+input_fol+'/temp/inner_left._81920.obj '+input_fol+'/surfaces/lh.smoothwm.to31.obj 0 100 0 0;')
os.system('adapt_object_mesh '+input_fol+'/temp/inner_right._81920.obj '+input_fol+'/surfaces/rh.smoothwm.to31.obj 0 100 0 0;')
os.system('/neuro/labs/grantlab/research/HyukJin_MRI/code/obj2asc '+input_fol+'/surfaces/lh.smoothwm.to31.obj '+input_fol+'/surfaces/lh.smoothwm.to31.asc;')
os.system('/neuro/labs/grantlab/research/HyukJin_MRI/code/obj2asc '+input_fol+'/surfaces/rh.smoothwm.to31.obj '+input_fol+'/surfaces/rh.smoothwm.to31.asc;')
os.system('transform_objects '+input_fol+'/surfaces/lh.smoothwm.to31.obj '+input_fol+'/recon_segmentation//recon_native.xfm '+input_fol+'/surfaces/lh.smoothwm.native.obj;')
os.system('transform_objects '+input_fol+'/surfaces/rh.smoothwm.to31.obj '+input_fol+'/recon_segmentation//recon_native.xfm '+input_fol+'/surfaces/rh.smoothwm.native.obj;')
os.system('transform_objects '+input_fol+'/surfaces/lh.smoothwm.to31.obj /neuro/labs/grantlab/research/HyukJin_MRI/Fetal_template/xfm/template-31toMNI.xfm '+input_fol+'/surfaces/lh.smoothwm.mni.obj;')
os.system('transform_objects '+input_fol+'/surfaces/rh.smoothwm.to31.obj /neuro/labs/grantlab/research/HyukJin_MRI/Fetal_template/xfm/template-31toMNI.xfm '+input_fol+'/surfaces/rh.smoothwm.mni.obj;')
def extrac():
os.system('nii2mnc '+input_fol+'/recon_segmentation/segmentation_to31_final.nii '+input_fol+'/temp/segmentation_to31_final.mnc;')
os.system('mincmath -clobber -eq -const 160 '+input_fol+'/temp/segmentation_to31_final.mnc '+input_fol+'/temp/inner_left.mnc;'
'mincmath -clobber -eq -const 161 '+input_fol+'/temp/segmentation_to31_final.mnc '+input_fol+'/temp/inner_right.mnc;')
os.system('singularity exec docker://fnndsc/pl-fetal-cp-surface-extract extract_cp --adapt_object_mesh 0,100,0,0 --mincmorph-iterations 1 --subsample '+input_fol+'/temp/ '+input_fol+'/temp/;')
os.system('adapt_object_mesh '+input_fol+'/temp/inner_left._81920.obj '+input_fol+'/surfaces/lh.smoothwm.to31.obj 0 100 0 0;')
os.system('adapt_object_mesh '+input_fol+'/temp/inner_right._81920.obj '+input_fol+'/surfaces/rh.smoothwm.to31.obj 0 100 0 0;')
os.system('/neuro/labs/grantlab/research/HyukJin_MRI/code/obj2asc '+input_fol+'/surfaces/lh.smoothwm.to31.obj '+input_fol+'/surfaces/lh.smoothwm.to31.asc;')
os.system('/neuro/labs/grantlab/research/HyukJin_MRI/code/obj2asc '+input_fol+'/surfaces/rh.smoothwm.to31.obj '+input_fol+'/surfaces/rh.smoothwm.to31.asc;')
os.system('transform_objects '+input_fol+'/surfaces/lh.smoothwm.to31.obj '+input_fol+'/recon_segmentation//recon_native.xfm '+input_fol+'/surfaces/lh.smoothwm.native.obj;')
os.system('transform_objects '+input_fol+'/surfaces/rh.smoothwm.to31.obj '+input_fol+'/recon_segmentation//recon_native.xfm '+input_fol+'/surfaces/rh.smoothwm.native.obj;')
os.system('transform_objects '+input_fol+'/surfaces/lh.smoothwm.to31.obj /neuro/labs/grantlab/research/HyukJin_MRI/Fetal_template/xfm/template-31toMNI.xfm '+input_fol+'/surfaces/lh.smoothwm.mni.obj;')
os.system('transform_objects '+input_fol+'/surfaces/rh.smoothwm.to31.obj /neuro/labs/grantlab/research/HyukJin_MRI/Fetal_template/xfm/template-31toMNI.xfm '+input_fol+'/surfaces/rh.smoothwm.mni.obj;')
#surface registration
def surf_reg():
#template_num=str(sys.arv[2])
for i in templ_num:
os.system('bestsurfreg.pl -clobber -min_control_mesh 80 -max_control_mesh 81920 -blur_coef 1.25 -neighbourhood_radius 2.8 -maximum_blur 1.9 /neuro/users/mri.team/fetal_mri/Surface_template/template-'+i+'/bh.smoothwm.mni.obj ./'+input_fol+'/surfaces/lh.smoothwm.mni.obj ./'+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.toT'+i+'.sm;')
os.system('bestsurfreg.pl -clobber -min_control_mesh 80 -max_control_mesh 81920 -blur_coef 1.25 -neighbourhood_radius 2.8 -maximum_blur 1.9 /neuro/users/mri.team/fetal_mri/Surface_template/template-'+i+'/bh.smoothwm.mni.obj ./'+input_fol+'/surfaces/rh.smoothwm.mni.obj ./'+input_fol+'/surfaces//template-'+i+'/rh.smoothwm.toT'+i+'.sm;')
#surface resample
def resampling():
for i in templ_num:
os.system('sphere_resample_obj -clobber ./'+input_fol+'/surfaces/lh.smoothwm.mni.obj ./'+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.toT'+i+'.sm ./'+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.mni.rsl'+i+'.obj;')
os.system('sphere_resample_obj -clobber ./'+input_fol+'/surfaces/rh.smoothwm.mni.obj ./'+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.toT'+i+'.sm ./'+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.mni.rsl'+i+'.obj;')
if i == "29":
os.system('cp ./'+input_fol+'/surfaces/template-29/lh.smoothwm.mni.rsl29.obj ./'+input_fol+'/surfaces/template-29/lh.smoothwm.mni.rsl.obj;')
os.system('cp ./'+input_fol+'/surfaces/template-29/rh.smoothwm.mni.rsl29.obj ./'+input_fol+'/surfaces/template-29/rh.smoothwm.mni.rsl.obj;')
else:
os.system('sphere_resample_obj -clobber ./'+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.mni.rsl'+i+'.obj /neuro/users/mri.team/fetal_mri/Surface_template/template-'+i+'/bh.smoothwm.T29.sm ./'+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.mni.rsl.obj;'
'sphere_resample_obj -clobber ./'+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.mni.rsl'+i+'.obj /neuro/users/mri.team/fetal_mri/Surface_template/template-'+i+'/bh.smoothwm.T29.sm ./'+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.mni.rsl.obj;')
os.system('transform_objects ./'+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.mni.rsl.obj /neuro/users/mri.team/fetal_mri/Surface_template/xfm/template-31toMNI_inv.xfm ./'+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.to31.rsl.obj;')
os.system('transform_objects ./'+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.mni.rsl.obj /neuro/users/mri.team/fetal_mri/Surface_template/xfm/template-31toMNI_inv.xfm ./'+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.to31.rsl.obj;')
os.system('transform_objects '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.to31.rsl.obj ./'+input_fol+'/recon_segmentation/recon_native.xfm ./'+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.native.rsl.obj;')
os.system('transform_objects '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.to31.rsl.obj ./'+input_fol+'/recon_segmentation/recon_native.xfm ./'+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.native.rsl.obj;')
#surface measures
def surf_meas():
for i in templ_num:
#sulcal depth
os.system('python3 /neuro/labs/grantlab/research/HyukJin_MRI/code/ADT/ADT_white_vFetal_final_rsl.py '+input_fol+'/surfaces/template-'+i+'/;')
os.system('depth_potential -smooth 10 '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.native.rsl.depth '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.mni.rsl.obj '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.native.rsl.depth.s10;')
os.system('depth_potential -smooth 10 '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.native.rsl.depth '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.mni.rsl.obj '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.native.rsl.depth.s10;')
os.system('depth_potential -smooth 20 '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.native.rsl.depth '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.mni.rsl.obj '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.native.rsl.depth.s20;')
os.system('depth_potential -smooth 20 '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.native.rsl.depth '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.mni.rsl.obj '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.native.rsl.depth.s20;')
# surface area
os.system('depth_potential -area_voronoi '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.native.rsl.obj '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.native.rsl.area;')
os.system('depth_potential -area_voronoi '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.native.rsl.obj '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.native.rsl.area;')
os.system('depth_potential -smooth 10 '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.native.rsl.area '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.mni.rsl.obj '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.native.rsl.area.s10;')
os.system('depth_potential -smooth 10 '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.native.rsl.area '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.mni.rsl.obj '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.native.rsl.area.s10;')
os.system('depth_potential -smooth 20 '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.native.rsl.area '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.mni.rsl.obj '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.native.rsl.area.s20;')
os.system('depth_potential -smooth 20 '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.native.rsl.area '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.mni.rsl.obj '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.native.rsl.area.s20;')
# mean curvature
os.system('depth_potential -mean_curvature '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.mni.rsl.obj '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.mni.rsl.mc;')
os.system('depth_potential -mean_curvature '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.mni.rsl.obj '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.mni.rsl.mc;')
os.system('depth_potential -smooth 10 '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.mni.rsl.mc '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.mni.rsl.obj '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.mni.rsl.mc.s10;')
os.system('depth_potential -smooth 10 '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.mni.rsl.mc '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.mni.rsl.obj '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.mni.rsl.mc.s10;')
os.system('depth_potential -smooth 20 '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.mni.rsl.mc '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.mni.rsl.obj '+input_fol+'/surfaces/template-'+i+'/lh.smoothwm.mni.rsl.mc.s20;')
os.system('depth_potential -smooth 20 '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.mni.rsl.mc '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.mni.rsl.obj '+input_fol+'/surfaces/template-'+i+'/rh.smoothwm.mni.rsl.mc.s20;')
#s5 calculations inside /surfaces folder
os.system('python3 /neuro/labs/grantlab/research/HyukJin_MRI/code/ADT/ADT_white_vFetal_final.py '+input_fol+'/surfaces/;')
os.system('depth_potential -smooth 5 '+input_fol+'/surfaces/lh.smoothwm.native.depth '+input_fol+'/surfaces/lh.smoothwm.mni.obj '+input_fol+'/surfaces/lh.smoothwm.native.depth.s5;')
os.system('depth_potential -smooth 5 '+input_fol+'/surfaces/rh.smoothwm.native.depth '+input_fol+'/surfaces/rh.smoothwm.mni.obj '+input_fol+'/surfaces/rh.smoothwm.native.depth.s5;')
os.system('depth_potential -area_voronoi '+input_fol+'/surfaces/lh.smoothwm.native.obj '+input_fol+'/surfaces/lh.smoothwm.native.area;')
os.system('depth_potential -area_voronoi '+input_fol+'/surfaces/rh.smoothwm.native.obj '+input_fol+'/surfaces/rh.smoothwm.native.area;')
os.system('depth_potential -smooth 5 '+input_fol+'/surfaces/lh.smoothwm.native.area '+input_fol+'/surfaces/lh.smoothwm.mni.obj '+input_fol+'/surfaces/lh.smoothwm.native.area.s5;')
os.system('depth_potential -smooth 5 '+input_fol+'/surfaces/rh.smoothwm.native.area '+input_fol+'/surfaces/rh.smoothwm.mni.obj '+input_fol+'/surfaces/rh.smoothwm.native.area.s5;')
os.system('depth_potential -mean_curvature '+input_fol+'/surfaces/lh.smoothwm.mni.obj '+input_fol+'/surfaces/lh.smoothwm.mni.mc;')
os.system('depth_potential -mean_curvature '+input_fol+'/surfaces/rh.smoothwm.mni.obj '+input_fol+'/surfaces/rh.smoothwm.mni.mc;')
os.system('depth_potential -smooth 5 '+input_fol+'/surfaces/lh.smoothwm.mni.mc '+input_fol+'/surfaces/lh.smoothwm.mni.obj '+input_fol+'/surfaces/lh.smoothwm.mni.mc.s5;')
os.system('depth_potential -smooth 5 '+input_fol+'/surfaces/rh.smoothwm.mni.mc '+input_fol+'/surfaces/rh.smoothwm.mni.obj '+input_fol+'/surfaces/rh.smoothwm.mni.mc.s5;')
# whole brain depth, area, and curvature -> txt
os.system('echo `python3 /neuro/labs/grantlab/research/HyukJin_MRI/code/vertex_mean_sum.py -sum '+input_fol+'/surfaces/lh.smoothwm.native.area.s5` '
'`python3 /neuro/labs/grantlab/research/HyukJin_MRI/code/vertex_mean_sum.py -sum '+input_fol+'/surfaces/rh.smoothwm.native.area.s5` '
'`python3 /neuro/labs/grantlab/research/HyukJin_MRI/code/vertex_mean_sum.py -mean '+input_fol+'/surfaces/lh.smoothwm.native.depth.s5` '
'`python3 /neuro/labs/grantlab/research/HyukJin_MRI/code/vertex_mean_sum.py -mean '+input_fol+'/surfaces/rh.smoothwm.native.depth.s5` '
'`python3 /neuro/labs/grantlab/research/HyukJin_MRI/code/vertex_mean_sum.py -ab_mean '+input_fol+'/surfaces/lh.smoothwm.mni.mc.s5` '
'`python3 /neuro/labs/grantlab/research/HyukJin_MRI/code/vertex_mean_sum.py -ab_mean '+input_fol+'/surfaces/rh.smoothwm.mni.mc.s5` > '+input_fol+'/surfaces/Area_Depth_aMC.txt;')
# verify surface measures
os.system('mkdir '+input_fol+'/surfaces/verify')
os.system('cp '+input_fol+'/surfaces/*.mni.obj* '+input_fol+'/surfaces/*.s5* '+input_fol+'/surfaces/verify;')
os.system('apptainer exec docker://fnndsc/pl-surfigures:latest surfigures --range .area.s5:0.0:1.0,.depth.s5:0.0:20.0,.mc.s5:-0.5:0.5 -s .s5 -o s5.png surfaces/verify surfaces/verify')
#volume measures
def vol_meas():
seg_final= input_fol+'/recon_segmentation/segmentation_to31_final.nii'
final_nii= nib.load(seg_final)
img_data= final_nii.get_fdata()
vox_inRange_1 = ((img_data > 159) & (img_data < 161)).sum()
vox_inRange_2 = ((img_data > 160) & (img_data < 162)).sum()
vox_inRange_3 = ((img_data > 41) & (img_data < 43)).sum()
vox_inRange_4 = ((img_data > 0) & (img_data < 2)).sum()
print("num voxels:", vox_inRange_1, vox_inRange_2, vox_inRange_3, vox_inRange_4)
voxel_sizes = np.abs(final_nii.header.get_zooms())
print("vox size:", voxel_sizes)
vol1 = vox_inRange_1 * np.prod(voxel_sizes)
vol2 = vox_inRange_2 * np.prod(voxel_sizes)
vol3 = vox_inRange_3 * np.prod(voxel_sizes)
vol4 = vox_inRange_4 * np.prod(voxel_sizes)
xfm_path = input_fol+'/recon_segmentation/recon_native.xfm'
os.system('xfm2param '+input_fol+'/recon_segmentation/recon_native.xfm | grep scale | cut -d" " -f11 > '+input_fol+'/temp/temp2.txt;')
os.system('xfm2param '+input_fol+'/recon_segmentation/recon_native.xfm | grep scale | cut -d" " -f15 >> '+input_fol+'/temp/temp2.txt;')
os.system('xfm2param '+input_fol+'/recon_segmentation/recon_native.xfm | grep scale | cut -d" " -f19 >> '+input_fol+'/temp/temp2.txt;')
with open(input_fol+'/temp/temp2.txt') as temp2:
scale_temp = [0,0,0]
scale_temp=temp2.readlines()
scale_av = float(scale_temp[0]) * float(scale_temp[1]) * float(scale_temp[2])
print(scale_av)
v1xScale = (vol1 * scale_av)
v2xScale = (vol2 * scale_av)
v3xScale = (vol3 * scale_av)
v4xScale = (vol4 * scale_av)
with open(input_fol+'/recon_segmentation/Volume_measures.txt', "w") as file:
file.write(str(v1xScale) + "\n" + str(v2xScale)+ "\n" + str(v3xScale) + "\n" +str(v4xScale) )
#gyrification index
def GI():
os.system('mkdir ./'+input_fol+'/temp/hull/;')
os.system('mri_distance_transform ./'+input_fol+'/recon_segmentation/segmentation_to31_final.nii 160 10 1 ./'+input_fol+'/temp/lh.dist10.nii;'
'mri_threshold ./'+input_fol+'/temp/lh.dist10.nii 10 ./'+input_fol+'/temp/lh.dist10.mask.nii;'
'mri_distance_transform ./'+input_fol+'/temp/lh.dist10.mask.nii 0 10 2 ./'+input_fol+'/temp/lh.dist10.mask.dist10.nii;'
'fslmaths ./'+input_fol+'/temp/lh.dist10.mask.dist10.nii -mul -1 ./'+input_fol+'/temp/lh.dist10.mask.dist10.inv.nii;'
'gunzip ./'+input_fol+'/temp/lh.dist10.mask.dist10.inv.nii.gz;'
'mri_threshold ./'+input_fol+'/temp/lh.dist10.mask.dist10.inv.nii 10 ./'+input_fol+'/temp/lh.closing.nii;')
os.system('mri_distance_transform ./'+input_fol+'/recon_segmentation/segmentation_to31_final.nii 161 10 1 ./'+input_fol+'/temp/rh.dist10.nii;'
'mri_threshold ./'+input_fol+'/temp/rh.dist10.nii 10 ./'+input_fol+'/temp/rh.dist10.mask.nii;'
'mri_distance_transform ./'+input_fol+'/temp/rh.dist10.mask.nii 0 10 2 ./'+input_fol+'/temp/rh.dist10.mask.dist10.nii;'
'fslmaths ./'+input_fol+'/temp/rh.dist10.mask.dist10.nii -mul -1 ./'+input_fol+'/temp/rh.dist10.mask.dist10.inv.nii;'
'gunzip ./'+input_fol+'/temp/rh.dist10.mask.dist10.inv.nii.gz;'
'mri_threshold ./'+input_fol+'/temp/rh.dist10.mask.dist10.inv.nii 10 ./'+input_fol+'/temp/rh.closing.nii;')
os.system('nii2mnc ./'+input_fol+'/temp/lh.closing.nii ./'+input_fol+'/temp/lh.closing.mnc;'
'nii2mnc ./'+input_fol+'/temp/rh.closing.nii ./'+input_fol+'/temp/rh.closing.mnc;')
os.system('mincmath -clobber -gt -const 0 ./'+input_fol+'/temp/lh.closing.mnc ./'+input_fol+'/temp/hull/closing_bin_left.mnc;'
'mincmath -clobber -gt -const 0 ./'+input_fol+'/temp/rh.closing.mnc ./'+input_fol+'/temp/hull/closing_bin_right.mnc;')
os.system('singularity exec docker://fnndsc/pl-fetal-cp-surface-extract extract_cp --adapt_object_mesh 0,100,0,0 '+input_fol+'/temp/hull/ '+input_fol+'/temp/hull/;')
os.system('cp '+input_fol+'/temp/hull/closing_bin_left._81920.obj '+input_fol+'/temp/lh.hull.to31.obj;'
'cp '+input_fol+'/temp/hull/closing_bin_right._81920.obj '+input_fol+'/temp/rh.hull.to31.obj;')
os.system('measure_surface_area ./'+input_fol+'/surfaces/lh.smoothwm.to31.obj > ./'+input_fol+'/temp/GI_inf2.txt;'
'measure_surface_area ./'+input_fol+'/temp/lh.hull.to31.obj >> ./'+input_fol+'/temp/GI_inf2.txt;'
'measure_surface_area ./'+input_fol+'/surfaces/rh.smoothwm.to31.obj >> ./'+input_fol+'/temp/GI_inf2.txt;'
'measure_surface_area ./'+input_fol+'/temp/rh.hull.to31.obj >> ./'+input_fol+'/temp/GI_inf2.txt;')
with open(input_fol+'/temp/GI_inf2.txt') as GI_temp:
temp=GI_temp.read()
temp=temp.split('Area: ');
bh_surf= float(temp[1])+float(temp[3])
bh_hull= float(temp[2])+float(temp[4])
lh_GI=float(temp[1])/float(temp[2])
rh_GI=float(temp[3])/float(temp[4])
GI_temp.close
bh_GI=str(bh_surf/bh_hull)
lh_GI=str(lh_GI)
rh_GI=str(rh_GI)
os.system('echo '+lh_GI+' '+rh_GI+' '+bh_GI+' > ./'+input_fol+'/surfaces/GI_info_final.txt;')
def main():
args = parser.parse_args()
print(args)
global input_fol
input_fol = args.input_fol ## input_fol should be: ./$file
if not os.path.exists(input_fol+'/surfaces/'): #/ use os.mkdir()?
os.system('mkdir '+input_fol+'/surfaces/')
if not os.path.exists(input_fol+'/temp/'):
os.system('mkdir '+input_fol+'/temp/')
global templ_num
global i
templ_num=("29","31","adult") ##default to template 29
for i in templ_num:
os.makedirs(input_fol+'/surfaces/template-'+i+'/', exist_ok=True)
extraction = args.extrac
from_reg = args.reg__
registration = args.surf_reg
resample = args.resampling
S_meas = args.surf_meas
V_meas = args.vol_meas
gi = args.GI
allSteps = args.all
all_young = args.all_young
rnum=("1","2","3")
#creates recon_native.xfm if not already inside appropriate folder(s)
for r in rnum:
if os.path.exists(input_fol+'/temp_recon_'+r) and not os.path.exists(input_fol+'/temp_recon_'+r+'/recon_native.xfm'):
os.system('convert_xfm -omat '+input_fol+'/temp_recon_'+r+'/recon_to31_inv.xfm -inverse '+input_fol+'/temp_recon_'+r+'/recon_to31.xfm;')
os.system('echo `avscale '+input_fol+'/temp_recon_'+r+'/recon_to31_inv.xfm | grep Scales` > '+input_fol+'/temp/temp.txt;')
scales=open(input_fol+'/temp/temp.txt', encoding='utf-8')
scales=scales.read()
os.system('param2xfm -clobber -scales '+scales[16:-1]+' '+input_fol+'/temp_recon_'+r+'/recon_native.xfm;')
if os.path.exists(input_fol+'/temp_recon_'+r+'/segmentation_to31_final.nii') and not os.path.exists(input_fol+'/recon_segmentation/segmentation_to31_final.nii'):
##use os.rename instead of mv?
os.system('mv -T '+input_fol+'/temp_recon_'+r+' '+input_fol+'/recon_segmentation')
print('segmentation_to31_final.nii file found in temp_recon_'+r+' and folder renamed to "recon_segmentation"')
if not os.path.exists(input_fol+'/recon_segmentation/recon_native.xfm'):
os.system('convert_xfm -omat '+input_fol+'/recon_segmentation/recon_to31_inv.xfm -inverse '+input_fol+'/recon_segmentation/recon_to31.xfm;')
os.system('echo `avscale '+input_fol+'/recon_segmentation/recon_to31_inv.xfm | grep Scales` > '+input_fol+'/temp/temp.txt;')
scales=open(input_fol+'/temp/temp.txt', encoding='utf-8')
scales=scales.read()
os.system('param2xfm -clobber -scales '+scales[16:-1]+' '+input_fol+'/recon_segmentation/recon_native.xfm;')
if extraction == True:
extrac()
print('surface extraction step complete')
if from_reg == True:
surf_reg()
resampling()
surf_meas()
vol_meas()
GI()
if registration == True:
surf_reg()
if resample == True:
resampling()
if S_meas == True:
surf_meas()
if V_meas == True:
vol_meas()
if gi == True:
GI()
if all_young == True:
extraction_woSubsample()
surf_reg()
resampling()
surf_meas()
vol_meas()
GI()
if allSteps == True:
extrac()
surf_reg()
resampling()
surf_meas()
vol_meas()
GI()
if __name__ == '__main__':
main()