keyword stringclasses 7
values | repo_name stringlengths 8 98 | file_path stringlengths 4 244 | file_extension stringclasses 29
values | file_size int64 0 84.1M | line_count int64 0 1.6M | content stringlengths 1 84.1M ⌀ | language stringclasses 14
values |
|---|---|---|---|---|---|---|---|
3D | hku-mars/ImMesh | src/meshing/tinycolormap.hpp | .hpp | 104,096 | 2,467 | /*
MIT License
Copyright (c) 2018-2020 Yuki Koyama
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, ... | Unknown |
3D | hku-mars/ImMesh | src/meshing/mesh_rec_display.cpp | .cpp | 12,849 | 327 | #define STB_IMAGE_WRITE_IMPLEMENTATION
#define STBI_MSC_SECURE_CRT
#include "mesh_rec_display.hpp"
#include "tools/openGL_libs/gl_draw_founction.hpp"
#include "tools_timer.hpp"
#include "tinycolormap.hpp"
#include "tools/openGL_libs/openGL_camera.hpp"
extern Global_map g_map_rgb_pts_mesh;
extern Tri... | C++ |
3D | hku-mars/ImMesh | src/meshing/mesh_rec_geometry.cpp | .cpp | 16,170 | 435 | #include "mesh_rec_geometry.hpp"
#include "tinycolormap.hpp"
#include <pcl/io/ply_io.h>
#include <tbb/tbb.h>
#include <tbb/blocked_range.h>
#include <tbb/parallel_for.h>
#include <pcl/kdtree/kdtree_flann.h>
extern double g_color_val_min, g_color_val_max;
extern int g_force_update_flag;
extern Global_map g_m... | C++ |
3D | hku-mars/ImMesh | src/meshing/delaunay/openCV_subdiv2d_index.hpp | .hpp | 1,560 | 52 | #pragma once
#include <opencv2/opencv.hpp>
class Subdiv2DIndex : public cv::Subdiv2D
{
public :
Subdiv2DIndex(cv::Rect rectangle);
//Source code of Subdiv2D: https://github.com/opencv/opencv/blob/master/modules/imgproc/src/subdivision2d.cpp#L762
//The implementation tweaks getTrianglesList() so that only the in... | Unknown |
3D | hku-mars/ImMesh | src/meshing/optical_flow/lkpyramid.cpp | .cpp | 34,391 | 821 | /*M///////////////////////////////////////////////////////////////////////////////////////
//
// IMPORTANT: READ BEFORE DOWNLOADING, COPYING, INSTALLING OR USING.
//
// By downloading, copying, installing or using the software you agree to this license.
// If you do not agree to this license, do not download, instal... | C++ |
3D | hku-mars/ImMesh | src/meshing/optical_flow/lkpyramid.hpp | .hpp | 6,321 | 135 | // This file is modified from lkpyramid.hpp of openCV
#pragma once
#include "opencv2/core.hpp"
#include "opencv2/highgui.hpp"
#include "opencv2/video/tracking.hpp"
#include "opencv2/imgproc.hpp"
#define CV_CPU_HAS_SUPPORT_SSE2 1
#define USING_OPENCV_TBB 1
#include "opencv2/core/hal/intrin.hpp"
#include "tools_logger.hp... | Unknown |
3D | hku-mars/ImMesh | src/meshing/r3live/triangle.cpp | .cpp | 3,178 | 80 | #include "triangle.hpp"
vec_3 Triangle_manager::get_triangle_center(const Triangle_ptr& tri_ptr)
{
vec_3 triangle_pos = ( m_pointcloud_map->m_rgb_pts_vec[ tri_ptr->m_tri_pts_id[ 0 ] ]->get_pos() +
m_pointcloud_map->m_rgb_pts_vec[ tri_ptr->m_tri_pts_id[ 1 ] ]->get_pos() +
... | C++ |
3D | hku-mars/ImMesh | src/meshing/r3live/pointcloud_rgbd.cpp | .cpp | 39,836 | 958 | /*
This code is the implementation of our paper "R3LIVE: A Robust, Real-time, RGB-colored,
LiDAR-Inertial-Visual tightly-coupled state Estimation and mapping package".
Author: Jiarong Lin < ziv.lin.ljr@gmail.com >
If you use any code of this repo in your academic research, please cite at least
one of our papers:
[1... | C++ |
3D | hku-mars/ImMesh | src/meshing/r3live/image_frame.hpp | .hpp | 11,622 | 315 | /*
This code is the implementation of our paper "R3LIVE: A Robust, Real-time, RGB-colored,
LiDAR-Inertial-Visual tightly-coupled state Estimation and mapping package".
Author: Jiarong Lin < ziv.lin.ljr@gmail.com >
If you use any code of this repo in your academic research, please cite at least
one of our papers:
... | Unknown |
3D | hku-mars/ImMesh | src/meshing/r3live/triangle.hpp | .hpp | 14,546 | 430 | #pragma once
#include <set>
#include <unordered_set>
#include "tools_kd_hash.hpp"
#include "pointcloud_rgbd.hpp"
// class RGB_pts;
// class RGB_Voxel;
class Global_map;
class Triangle
{
public:
int m_tri_pts_id[ 3 ] = { 0 };
vec_3 m_normal = vec_3( 0, 0, 0 );
int m_projected_texture_id = 0;
vec... | Unknown |
3D | hku-mars/ImMesh | src/meshing/r3live/image_frame.cpp | .cpp | 13,935 | 402 | /*
This code is the implementation of our paper "R3LIVE: A Robust, Real-time, RGB-colored,
LiDAR-Inertial-Visual tightly-coupled state Estimation and mapping package".
Author: Jiarong Lin < ziv.lin.ljr@gmail.com >
If you use any code of this repo in your academic research, please cite at least
one of our papers:
... | C++ |
3D | hku-mars/ImMesh | src/meshing/r3live/pointcloud_rgbd.hpp | .hpp | 15,825 | 375 | /*
This code is the implementation of our paper "R3LIVE: A Robust, Real-time, RGB-colored,
LiDAR-Inertial-Visual tightly-coupled state Estimation and mapping package".
Author: Jiarong Lin < ziv.lin.ljr@gmail.com >
If you use any code of this repo in your academic research, please cite at least
one of our papers:
[1... | Unknown |
3D | Aswendt-Lab/AIDAmri | AIDAmri_workshop.ipynb | .ipynb | 175,298 | 2,986 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Table of contents\n",
"* [Before we start](#intro)\n",
" - [Prerequisites](#prereq)\n",
" - [About the notebook](#aboutnb)\n",
" - [Test data](#testd)\n",
"* [From build to launch](#fbtl)\n",
" - [... | Unknown |
3D | Aswendt-Lab/AIDAmri | fslinstaller_mod.py | .py | 103,777 | 3,100 | #!/usr/bin/python
from __future__ import print_function
import collections
import csv
import errno
import getpass
import itertools
import json
import locale
import os
import platform
import threading
import time
import shlex
import socket
import sys
import readline
import tempfile
import re
import fileinput
# py3
tr... | Python |
3D | Aswendt-Lab/AIDAmri | bin/__init__.py | .py | 33 | 2 | from PV2NIfTiConverter import *
| Python |
3D | Aswendt-Lab/AIDAmri | bin/conv2Nifti_auto.py | .py | 20,037 | 478 | """
Created on 18/10/2023
@author: Marc Schneider
AG Neuroimaging and Neuroengineering of Experimental Stroke
Department of Neurology, University Hospital Cologne
This script automates the conversion from the raw bruker data format to the NIfTI
format for the whole dataset using brkraw. The raw
data needs to be store... | Python |
3D | Aswendt-Lab/AIDAmri | bin/batchProc.py | .py | 21,057 | 443 | """
Created on 18/11/2020
@author: Marc Schneider
AG Neuroimaging and Neuroengineering of Experimental Stroke
Department of Neurology, University Hospital Cologne
This script runs every needed script for all (pre-)processing and registration
steps. The data needs to be ordered like after Bruker2NIfTI conversion:
proj... | Python |
3D | Aswendt-Lab/AIDAmri | bin/5.1_ROI_analysis/proc_tools.py | .py | 11,672 | 257 | '''
Created on 29.09.2020
Author:
Michael Diedenhofen
Max Planck Institute for Metabolism Research, Cologne
'''
from __future__ import print_function
import csv
import os
import sys
import nibabel as nib
from datetime import datetime
# directories
lib_in_dir = r'C:\Users\Public\Linux\shared_folder\AIDAmri\lib'
pr... | Python |
3D | Aswendt-Lab/AIDAmri | bin/5.1_ROI_analysis/04_examine_rois.py | .py | 1,858 | 62 | '''
Created on 25.08.2020
Author:
Michael Diedenhofen
Max Planck Institute for Metabolism Research, Cologne
Description:
Helper tool to compare the number of voxels included in the peri-infarct region for each subject.
'''
from __future__ import print_function
try:
zrange = xrange
except NameError:
zrange =... | Python |
3D | Aswendt-Lab/AIDAmri | bin/5.1_ROI_analysis/02_apply_xfm_process.py | .py | 17,479 | 346 | '''
Created on 19.10.2020
Author:
Michael Diedenhofen
Max Planck Institute for Metabolism Research, Cologne
Description:
Pre-requisite: 01_dilate_mask_process.py
Result: for all time points the peri-infarct masks will be aligned in the rsfMRI and DTI space
Two scans of the same session can be aligned to each other w... | Python |
3D | Aswendt-Lab/AIDAmri | bin/5.1_ROI_analysis/create_seed_rois.py | .py | 6,520 | 182 | '''
Created on 20.08.2020
Author:
Michael Diedenhofen
Max Planck Institute for Metabolism Research, Cologne
'''
from __future__ import print_function
try:
zrange = xrange
except NameError:
zrange = range
import os
import sys
import numpy as np
import nibabel as nib
import proc_tools as pt
def create_rois... | Python |
3D | Aswendt-Lab/AIDAmri | bin/5.1_ROI_analysis/fsl_mean_ts.py | .py | 2,881 | 92 | '''
Created on 31.08.2020
Author:
Michael Diedenhofen
Max Planck Institute for Metabolism Research, Cologne
'''
from __future__ import print_function
try:
zrange = xrange
except NameError:
zrange = range
import os
import sys
import numpy as np
import scipy.io as sio
import proc_tools as pt
def mean_ts(pa... | Python |
3D | Aswendt-Lab/AIDAmri | bin/5.1_ROI_analysis/apply_xfm.py | .py | 5,919 | 178 | '''
Created on 20.08.2020
Author:
Michael Diedenhofen
Max Planck Institute for Metabolism Research, Cologne
'''
from __future__ import print_function
try:
zrange = xrange
except NameError:
zrange = range
import os
import sys
import numpy as np
import proc_tools as pt
def get_mat_flip_x_z(data_dims, voxel... | Python |
3D | Aswendt-Lab/AIDAmri | bin/5.1_ROI_analysis/pv_parser.py | .py | 13,157 | 417 | '''
Created on 20.08.2020
Author:
Michael Diedenhofen
Max Planck Institute for Metabolism Research, Cologne
Read Bruker ParaVision JCAMP parameter files (e.g. acqp, method, visu_pars).
'''
from __future__ import print_function
VERSION = 'pv_parser.py v 1.0.2 20200820'
import re
import sys
import collections
impo... | Python |
3D | Aswendt-Lab/AIDAmri | bin/5.1_ROI_analysis/01_dilate_mask_process.py | .py | 9,824 | 230 | '''
Created on 19.10.2020
Author:
Michael Diedenhofen
Max Planck Institute for Metabolism Research, Cologne
Description:
Pre-requisits: stroke mask was defined at post stroke day 7 (P7)
Result: for all time points the peri-infarct mask is created aligned to the individual T2w MRI data
1. Time point P7: For each subj... | Python |
3D | Aswendt-Lab/AIDAmri | bin/5.1_ROI_analysis/03_create_seed_rois_process.py | .py | 12,461 | 253 | '''
Created on 19.10.2020
Author:
Michael Diedenhofen
Max Planck Institute for Metabolism Research, Cologne
Description:
Pre-requisite: 02_apply_xfm_process.py
Result:
rsfMRI - a Matlab file which contains two text files: 1) for each region one column with the averaged rsfMRI time series and 2) the atlas labels names... | Python |
3D | Aswendt-Lab/AIDAmri | bin/5.1_ROI_analysis/dilate_mask.py | .py | 1,916 | 73 | '''
Created on 20.08.2020
Author:
Michael Diedenhofen
Max Planck Institute for Metabolism Research, Cologne
'''
from __future__ import print_function
try:
zrange = xrange
except NameError:
zrange = range
import os
import sys
import numpy as np
from scipy import ndimage
import proc_tools as pt
def circle... | Python |
3D | Aswendt-Lab/AIDAmri | bin/5.1_ROI_analysis/pv_reader.py | .py | 19,580 | 491 | '''
Created on 19.10.2020
Author:
Michael Diedenhofen
Max Planck Institute for Metabolism Research, Cologne
Read Bruker ParaVision data (2dseq) and save as NIfTI file.
Create a b-table text file with b-values and directions for diffusion data.
'''
from __future__ import print_function
try:
zrange = xrange
excep... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.3_fMRIActivity/getSingleRegTable.py | .py | 5,280 | 138 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import sys,os
import numpy as np
import glob
import shutil
import parReader
import i32Reader
def findData(path,addon):
reg_list = []
fileALL = glob.iglob(path+'/'+addon... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.3_fMRIActivity/correlate_matrix.py | .py | 914 | 23 | import numpy as np
import scipy.io as io
from scipy.stats import pearsonr
def calculate_p_corr_matrix(data, lines, output_paths):
(rows, cols) = np.shape(data)
correlation_matrix = np.zeros((cols,cols))
p_value_matrix = np.zeros((cols,cols))
for i in range(cols):
for j in range(i+1, cols):
... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.3_fMRIActivity/regress.py | .py | 11,859 | 330 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import sys,os
import nibabel as nii
import numpy as np
import nipype.interfaces.fsl as fsl
import glob
import shutil
from pathlib import Path
def scaleBy10(input_path,inv):
... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.3_fMRIActivity/process_fMRI.py | .py | 13,283 | 363 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import sys, os
import nipype.interfaces.fsl as fsl
import nibabel as nii
import numpy as np
import glob
import shutil
import regress
import getSingleRegTable
import scipy.misc as... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.3_fMRIActivity/parReader.py | .py | 1,205 | 51 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import numpy as np
import os,sys
def getPar(filename):
## Open the text file.
fileID = open(filename,'r')
# Read columns of data according to the format.
fileID... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.3_fMRIActivity/correlate_seed_voxels.py | .py | 5,780 | 155 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
from __future__ import print_function
import argparse
import os
import sys
import numpy as np
import nibabel as nib
from datetime import datetime
def get_date():
now = dat... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.3_fMRIActivity/create_seed_rois.py | .py | 9,633 | 272 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
from __future__ import print_function
import argparse
import os
import sys
import numpy as np
import nibabel as nib
from datetime import datetime
def startSeedPoint(in_labels,in... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.3_fMRIActivity/fsl_mean_ts.py | .py | 6,495 | 173 | """
Created on 07.12.2015
@author: michaeld
"""
from __future__ import print_function
import argparse
import os
import sys
import numpy as np
import nibabel as nib
import scipy.io as io
import correlate_matrix
from datetime import datetime
def start_fsl_mean_ts(sPathData,sPathMask,labelNames,postTxt):
# input... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.3_fMRIActivity/getRegrTable.py | .py | 5,398 | 135 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import sys,os
import numpy as np
import glob
import parReader
import i32Reader
def findData(path,addon):
reg_list = []
fileALL = glob.iglob(path+'/'+addon, recursive=True... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.3_fMRIActivity/peakdet.py | .py | 2,337 | 87 | """
Converted from MATLAB script at http://billauer.co.il/peakdet.html
Returns two arrays
function [maxtab, mintab]=peakdet(v, delta, x)
%PEAKDET Detect peaks in a vector
% [MAXTAB, MINTAB] = PEAKDET(V, DELTA) finds the local
% maxima and minima ("peaks") in the vector V.
% MAXTAB and MINTAB cons... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.3_fMRIActivity/plotfMRI_mat.py | .py | 2,137 | 76 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import matplotlib.pyplot as plt
import os, sys
import numpy as np
import scipy.io as sio
np.seterr(divide='ignore', invalid='ignore')
import seaborn as sns
def matrixMaker(ma... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.3_fMRIActivity/i32Reader.py | .py | 5,214 | 153 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import sys,os
import numpy as np
import peakdet as pk
import scipy.signal as sc
# noinspection PyTypeChecker
def getI32(file_name,numberOfSlices,numberOfAllRepitionsParTable)... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.2.1_DTIdata_extract/iterativeRun.py | .py | 1,074 | 45 | '''
Created on 08.04.2019
@author: Niklas Pallast
process all DTI data
'''
import glob
import os
import numpy as np
def findData(path):
regAtlas_list = []
fileALL = glob.iglob(path + '/P*/S*/DTI/DSI_studio/*_rsfMRISplit_scaled.nii.gz', recursive=True)
for filename in fileALL:
regAtlas_list.ap... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.2.1_DTIdata_extract/iterativeRun_MA_peri-infarct_ROIs.py | .py | 2,326 | 66 | '''
Created on 08.04.2019
Updated: 26.09.2020
@author: Niklas Pallast and Markus Aswendt
process all DTI data
'''
import glob
import os
import numpy as np
def findData(path):
regAtlas_list = []
fileALL = glob.iglob(path + '/GV*/DTI/DSI_studio/*mod_peri_scaled.nii.gz', recursive=True)
for filename in f... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.2.1_DTIdata_extract/DTIdata_extract.py | .py | 3,384 | 102 | """"
Created on 06.04.2019
@authors: Niklas Pallast
"""
import os
import sys
import argparse
import numpy as np
import nibabel as nii
def getOutfile(roi_file,img_file):
imgName = os.path.basename(img_file)
baseName = str.split(os.path.basename(roi_file),'.')[0]
dtiParam = str.split(imgName,'.')[-3]
... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.2.1_DTIdata_extract/iterativeRun_MA_stroke_mask.py | .py | 2,323 | 65 | '''
Created on 08.04.2019
Updated: 26.09.2020
@author: Niklas Pallast and Markus Aswendt
process all DTI data
'''
import glob
import os
import numpy as np
def findData(path):
regAtlas_list = []
fileALL = glob.iglob(path + '/GV*/DTI/DSI_studio/*StrokeMask_scaled.nii.gz', recursive=True)
for filename in... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.2.1_DTIdata_extract/iterativeRun_MA.py | .py | 2,331 | 66 | '''
Created on 08.04.2019
Updated: 26.09.2020
@author: Niklas Pallast and Markus Aswendt
process all DTI data
'''
import glob
import os
import numpy as np
def findData(path):
regAtlas_list = []
fileALL = glob.iglob(path + '/GV*/DTI/DSI_studio/*_rsfMRISplit_scaled.nii.gz', recursive=True)
for filename ... | Python |
3D | Aswendt-Lab/AIDAmri | bin/4.1_T2mapPreProcessing/registration_T2MAP.py | .py | 10,120 | 233 | """
Created on 11/09/2023
@author: Marc Schneider
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
Documentation preface, added 23/05/09 by Victor Vera Frazao:
This document is currently in revision for improvement and fixing.
Specifically changes are made to allow compatibility of... | Python |
3D | Aswendt-Lab/AIDAmri | bin/4.1_T2mapPreProcessing/t2map_data_extract.py | .py | 4,617 | 108 | import nibabel as nii
import numpy as np
import argparse
import os
import glob
import csv
import sys # Added import statement for sys module
def getOutfile(atlas_type, img_file, suffix):
imgName = os.path.basename(img_file)
t2map = str.split(imgName, '.')[-3]
acronym_name = os.path.basename(atlas_type).sp... | Python |
3D | Aswendt-Lab/AIDAmri | bin/4.1_T2mapPreProcessing/preProcessing_T2MAP.py | .py | 6,671 | 200 | """
Created on 11/09/2023
@author: Marc Schneider
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import nipype.interfaces.fsl as fsl
import os, sys
import nibabel as nii
import numpy as np
import applyMICO
import cv2
from pathlib import Path
import shutil
import subprocess
... | Python |
3D | Aswendt-Lab/AIDAmri | bin/4.1_T2mapPreProcessing/anisodiff.py | .py | 2,762 | 87 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import numpy as np
import scipy.ndimage
def applyFilter(im, num_iter, delta_t, kappa, option):
# Convert input image to float.
im.astype(float)
# PDE(partial diffe... | Python |
3D | Aswendt-Lab/AIDAmri | bin/4.1_T2mapPreProcessing/MICO.py | .py | 2,666 | 113 | """
@Article{li2014multiplicative,
author = {Li, Chunming and Gore, John C and Davatzikos, Christos},
title = {Multiplicative intrinsic component optimization (MICO) for MRI bias field estimation and tissue segmentation},
journal = {Magnetic resonance imaging},
year = {2014},
volume = {32},
... | Python |
3D | Aswendt-Lab/AIDAmri | bin/4.1_T2mapPreProcessing/applyMICO.py | .py | 5,649 | 216 | """
@Article{li2014multiplicative,
author = {Li, Chunming and Gore, John C and Davatzikos, Christos},
title = {Multiplicative intrinsic component optimization (MICO) for MRI bias field estimation and tissue segmentation},
journal = {Magnetic resonance imaging},
year = {2014},
volume = {32},
... | Python |
3D | Aswendt-Lab/AIDAmri | bin/2.1_T2PreProcessing/MICO.py | .py | 3,015 | 123 | """
@Article{li2014multiplicative,
author = {Li, Chunming and Gore, John C and Davatzikos, Christos},
title = {Multiplicative intrinsic component optimization (MICO) for MRI bias field estimation and tissue segmentation},
journal = {Magnetic resonance imaging},
year = {2014},
volume = {32},
... | Python |
3D | Aswendt-Lab/AIDAmri | bin/2.1_T2PreProcessing/t2_value_extraction.py | .py | 4,809 | 111 | import nibabel as nii
import numpy as np
import argparse
import os
import glob
import csv
import sys # Added import statement for sys module
def getOutfile(atlas_type, img_file, suffix):
imgName = os.path.basename(img_file)
t2map = str.split(imgName, '.')[-3]
acronym_name = os.path.basename(atlas_type).sp... | Python |
3D | Aswendt-Lab/AIDAmri | bin/2.1_T2PreProcessing/preProcessing_T2.py | .py | 5,376 | 184 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import nipype.interfaces.fsl as fsl
import os,sys
import nibabel as nii
import numpy as np
import applyMICO
import subprocess
import shutil
def reset_orientation(input_file):
... | Python |
3D | Aswendt-Lab/AIDAmri | bin/2.1_T2PreProcessing/registration_T2.py | .py | 12,410 | 282 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import sys,os
import numpy as np
import nibabel as nii
import glob
import subprocess
import shlex
def BET_2_MPIreg(inputVolume, stroke_mask,brain_template, allenBrain_template,a... | Python |
3D | Aswendt-Lab/AIDAmri | bin/2.1_T2PreProcessing/applyMICO.py | .py | 7,170 | 255 | """
@Article{li2014multiplicative,
author = {Li, Chunming and Gore, John C and Davatzikos, Christos},
title = {Multiplicative intrinsic component optimization (MICO) for MRI bias field estimation and tissue segmentation},
journal = {Magnetic resonance imaging},
year = {2014},
volume = {32},
... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.1_T2Processing/getIncidenceSize_par.py | .py | 8,846 | 255 |
"""
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import os,sys
import nibabel as nii
import glob
import numpy as np
import scipy.io as sc
import scipy.ndimage as ndimage
def find_nearest(array,value):
idx = (np.abs(arra... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.1_T2Processing/getIncidenceMap.py | .py | 4,056 | 107 | import os
import sys
import nibabel as nii
import glob
import numpy as np
import progressbar
import matplotlib
import matplotlib.pyplot as plt
# --- Fonts & Text Display ---
matplotlib.rcParams['svg.fonttype'] = 'none' #text remains editable in SVG
matplotlib.rcParams['pdf.fonttype'] = 42 # Editable text i... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.1_T2Processing/changSNR.py | .py | 1,856 | 69 | """ Changs's method
{chang2005automatic,
title={An automatic method for estimating noise-induced signal variance in magnitude-reconstructed magnetic resonance images},
author={Chang, Lin-Ching and Rohde, Gustavo K and Pierpaoli, Carlo},
booktitle={Medical Imaging},
pages={1136--1142},
year={2005},
organization={Interna... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.1_T2Processing/brummerSNR.py | .py | 1,682 | 59 | """ Brummer's Method
brummer1993automatic,
title={Automatic detection of brain contours in MRI data sets},
author={Brummer, Marijn E and Mersereau, Russell M and Eisner, Robert L and Lewine, Richard RJ},
journal={IEEE Transactions on medical imaging},
volume={12},
number={2},
pages={153--166},
year={1993},
publisher={I... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.1_T2Processing/getIncidenceSize.py | .py | 7,766 | 215 |
"""
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import os,sys
import nibabel as nii
import glob
import numpy as np
import scipy.io as sc
import scipy.ndimage as ndimage
def thresholding(volumeMR,maskImg,thres,k):
volumeM... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.1_T2Processing/sijbersSNR.py | .py | 1,797 | 62 | """"" Sijbers's method
sijbers2007automatic,
title={Automatic estimation of the noise variance from the histogram of a magnetic resonance image},
author={Sijbers, Jan and Poot, Dirk and den Dekker, Arnold J and Pintjens, Wouter},
journal={Physics in medicine and biology},
volume={52},
number={5},
pages={1335},
year={20... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.1_T2Processing/getSNR.py | .py | 2,537 | 88 | '''
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
'''
import os
import changSNR as ch
import brummerSNR as bm
import sijbersSNR as sj
import numpy as np
import glob
import nibabel as nii
def snrCalclualtor(input_file):
fileSNR ... | Python |
3D | Aswendt-Lab/AIDAmri | bin/helper_tools/DistributeStrokeMasks.py | .py | 2,937 | 64 | import os
import glob
import argparse
def main(inputPath):
log_file_path = os.path.join(inputPath, "missing_files_log.txt")
SearchPath = os.path.join(inputPath, "**", "anat", "*Stroke_mask.nii.gz")
List_of_Stroke_rois = glob.glob(SearchPath, recursive=True)
print(List_of_Stroke_rois)
for ss in List... | Python |
3D | Aswendt-Lab/AIDAmri | bin/helper_tools/reset_naming.py | .py | 2,944 | 79 | import os
import argparse
import glob
import re
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description=(
"This script prepares Bruker raw data before running "
"1_PV2NIfTiConverter/pv_conv2Nifti.py. "
"The raw data must follow the structure: projectfold... | Python |
3D | Aswendt-Lab/AIDAmri | bin/helper_tools/MRI_files_summarizer.py | .py | 1,999 | 54 | import os
import argparse
import glob
import pandas as pd
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='This script processes NIfTI files in a directory. It extracts relevant parts of the file name and creates a DataFrame.')
parser.add_argument('-i', '--input', required=True, help='P... | Python |
3D | Aswendt-Lab/AIDAmri | bin/helper_tools/ReorientBatch.py | .py | 13,057 | 430 | #!/usr/bin/env python3
import os
import sys
import subprocess
import shutil
import traceback
import argparse
import numpy as np
import nibabel as nib
from nibabel import orientations as nio
from typing import Optional
"""
Batch reorientation of NIfTI files within a BIDS-like directory structure.
Usage:
python R... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.2_DTIConnectivity/dsi_tools.py | .py | 17,129 | 426 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
Documentation preface, added 23/05/09 by Victor Vera Frazao:
This document is currently in revision for improvement and fixing.
Specifically changes are made to allow compatibility of ... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.2_DTIConnectivity/plotDTI_mat.py | .py | 3,742 | 127 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import matplotlib.pyplot as plt
import os, sys
import numpy as np
import scipy.io as sio
np.seterr(divide='ignore', invalid='ignore')
import seaborn as sns
def intersect_mtlb... | Python |
3D | Aswendt-Lab/AIDAmri | bin/3.2_DTIConnectivity/dsi_main.py | .py | 5,797 | 128 | #!/opt/env/bin/python
"""
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
from __future__ import print_function
import argparse
import os
import glob
import dsi_tools
import shutil
if __name__ == '__main__':
# default dsi studi... | Python |
3D | Aswendt-Lab/AIDAmri | bin/PV2NIfTiConverter/__init__.py | .py | 0 | 0 | null | Python |
3D | Aswendt-Lab/AIDAmri | bin/PV2NIfTiConverter/pv_parseBruker_md_np.py | .py | 11,946 | 345 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
from __future__ import print_function
import os,sys
import numpy as np
from dict2xml import createXML
# from string import split
def parsePV(filename):
"""
Parser fo... | Python |
3D | Aswendt-Lab/AIDAmri | bin/PV2NIfTiConverter/P2_IDLt2_mapping.py | .py | 12,514 | 344 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import os
from math import *
from lmfit import Minimizer, Parameters
import matplotlib.pyplot as plt
import nibabel as nii
import numpy as np
import progressbar
from .ReferenceMe... | Python |
3D | Aswendt-Lab/AIDAmri | bin/PV2NIfTiConverter/pv_conv2Nifti_bval_bvec.py | .py | 15,938 | 386 | """
Created on 10/08/2017
@author: Niklas Pallast, Markus Aswendt
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
from __future__ import print_function
import os
import time
import re
import sys
import numpy as np
import nibabel as nib
import nibabel.nifti1 as nii
import pv_... | Python |
3D | Aswendt-Lab/AIDAmri | bin/PV2NIfTiConverter/dict2xml.py | .py | 2,466 | 92 | """ Dictionary to XML - Library to convert a python dictionary to XML output
Copyleft (C) 2007 Pianfetti Maurizio <boymix81@gmail.com>
Package site : http://boymix81.altervista.org/files/dict2xml.tar.gz
Revision 1.0 2007/12/15 11:57:20 Maurizio
- First stable version
"""
__author__ = "Pianfetti Mau... | Python |
3D | Aswendt-Lab/AIDAmri | bin/PV2NIfTiConverter/pv_conv2Nifti.py | .py | 15,954 | 386 | """
Created on 10/08/2017
@author: Niklas Pallast, Marc Schneider, Markus Aswendt
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
from __future__ import print_function
import os
import time
import re
import sys
import numpy as np
import nibabel as nib
import nibabel.nifti1 a... | Python |
3D | Aswendt-Lab/AIDAmri | bin/PV2NIfTiConverter/ReferenceMethods/__init__.py | .py | 0 | 0 | null | Python |
3D | Aswendt-Lab/AIDAmri | bin/PV2NIfTiConverter/ReferenceMethods/changSNR.py | .py | 1,961 | 83 | """ Changs's method
{chang2005automatic,
title={An automatic method for estimating noise-induced signal variance in magnitude-reconstructed magnetic resonance images},
author={Chang, Lin-Ching and Rohde, Gustavo K and Pierpaoli, Carlo},
booktitle={Medical Imaging},
pages={1136--1142},
year={2005},
organization={Interna... | Python |
3D | Aswendt-Lab/AIDAmri | bin/PV2NIfTiConverter/ReferenceMethods/brummerSNR.py | .py | 1,775 | 71 | """ Brummer's Method
brummer1993automatic,
title={Automatic detection of brain contours in MRI data sets},
author={Brummer, Marijn E and Mersereau, Russell M and Eisner, Robert L and Lewine, Richard RJ},
journal={IEEE Transactions on medical imaging},
volume={12},
number={2},
pages={153--166},
year={1993},
publisher={I... | Python |
3D | Aswendt-Lab/AIDAmri | bin/PV2NIfTiConverter/ReferenceMethods/sijbersSNR.py | .py | 1,872 | 75 | """
Sijbers's method
sijbers2007automatic,
title={Automatic estimation of the noise variance from the histogram of a magnetic resonance image},
author={Sijbers, Jan and Poot, Dirk and den Dekker, Arnold J and Pintjens, Wouter},
journal={Physics in medicine and biology},
volume={52},
number={5},
pages={1335},
year={2007... | Python |
3D | Aswendt-Lab/AIDAmri | bin/PV2NIfTiConverter/ReferenceMethods/getSNR.py | .py | 2,348 | 89 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import os, sys
import changSNR as ch
import brummerSNR as bm
import sijbersSNR as sj
import numpy as np
import glob
import nibabel as nii
def snrCalclualtor(input_file, method... | Python |
3D | Aswendt-Lab/AIDAmri | bin/PV2NIfTiConverter/Alternative_pv_reader/pv_parser.py | .py | 13,157 | 417 | '''
Created on 20.08.2020
Author:
Michael Diedenhofen
Max Planck Institute for Metabolism Research, Cologne
Read Bruker ParaVision JCAMP parameter files (e.g. acqp, method, visu_pars).
'''
from __future__ import print_function
VERSION = 'pv_parser.py v 1.0.2 20200820'
import re
import sys
import collections
impo... | Python |
3D | Aswendt-Lab/AIDAmri | bin/PV2NIfTiConverter/Alternative_pv_reader/pv_reader.py | .py | 19,580 | 491 | '''
Created on 19.10.2020
Author:
Michael Diedenhofen
Max Planck Institute for Metabolism Research, Cologne
Read Bruker ParaVision data (2dseq) and save as NIfTI file.
Create a b-table text file with b-values and directions for diffusion data.
'''
from __future__ import print_function
try:
zrange = xrange
excep... | Python |
3D | Aswendt-Lab/AIDAmri | bin/2.2_DTIPreProcessing/registration_DTI.py | .py | 21,386 | 441 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
Documentation preface, added 23/05/09 by Victor Vera Frazao:
This document is currently in revision for improvement and fixing.
Specifically changes are made to allow compatibility of... | Python |
3D | Aswendt-Lab/AIDAmri | bin/2.2_DTIPreProcessing/preProcessing_DTI.py | .py | 6,660 | 196 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import nipype.interfaces.fsl as fsl
import os, sys
import nibabel as nii
import numpy as np
import applyMICO
import cv2
from pathlib import Path
import subprocess
import shutil
... | Python |
3D | Aswendt-Lab/AIDAmri | bin/2.2_DTIPreProcessing/anisodiff.py | .py | 2,762 | 87 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import numpy as np
import scipy.ndimage
def applyFilter(im, num_iter, delta_t, kappa, option):
# Convert input image to float.
im.astype(float)
# PDE(partial diffe... | Python |
3D | Aswendt-Lab/AIDAmri | bin/2.2_DTIPreProcessing/MICO.py | .py | 2,915 | 120 | """
@Article{li2014multiplicative,
author = {Li, Chunming and Gore, John C and Davatzikos, Christos},
title = {Multiplicative intrinsic component optimization (MICO) for MRI bias field estimation and tissue segmentation},
journal = {Magnetic resonance imaging},
year = {2014},
volume = {32},
... | Python |
3D | Aswendt-Lab/AIDAmri | bin/2.2_DTIPreProcessing/applyMICO.py | .py | 7,221 | 256 | """
@Article{li2014multiplicative,
author = {Li, Chunming and Gore, John C and Davatzikos, Christos},
title = {Multiplicative intrinsic component optimization (MICO) for MRI bias field estimation and tissue segmentation},
journal = {Magnetic resonance imaging},
year = {2014},
volume = {32},
... | Python |
3D | Aswendt-Lab/AIDAmri | bin/2.3_fMRIPreProcessing/preProcessing_fMRI.py | .py | 6,607 | 185 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import nipype.interfaces.fsl as fsl
import os,sys
import nibabel as nii
import numpy as np
import nipype.interfaces.ants as ants
from pathlib import Path
import subprocess
impor... | Python |
3D | Aswendt-Lab/AIDAmri | bin/2.3_fMRIPreProcessing/registration_rsfMRI.py | .py | 12,590 | 279 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import sys,os
import glob
import shutil as sh
import subprocess
import shlex
def regABA2rsfMRI(inputVolume, T2data, brain_template, brain_anno, splitAnno, splitAnno_rsfMRI, anno... | Python |
3D | Aswendt-Lab/AIDAmri | ARA/readXML_Lables.m | .m | 392 | 8 | function annotation50CHANGEDannolabelIDs = readXML_Lables(xml_file)
%% Import the data
[~, ~, annotation50CHANGEDannolabelIDs] = xlsread(xml_file);
annotation50CHANGEDannolabelIDs = annotation50CHANGEDannolabelIDs(2:end,5);
annotation50CHANGEDannolabelIDs = string(annotation50CHANGEDannolabelIDs);
annotation50CHANGEDa... | MATLAB |
3D | Aswendt-Lab/AIDAmri | ARA/getParentalARA.m | .m | 1,206 | 32 | %% Method generate a atlas with all parental regions of the given xlsx file
% getParentalARA('./annotation_label_IDs_valid.xlsx','./annotation/annotation.nii.gz')
function getParentalARA(xml_file,atlasNii_file)
addpath('./AllenBrainAPI-master/');
labelsStrArray = char(readXML_Lables(xml_file));
atlasData = load_nii(atl... | MATLAB |
3D | Aswendt-Lab/AIDAmri | ARA/download_ARA.py | .py | 2,738 | 85 | """
Created on 17/03/2020
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
More information can be found here:
http://alleninstitute.github.io/AllenSDK/_modules/allensdk/api/queries/reference_space_api.html
"""
import os
import nrrd # pip install pynrrd, if... | Python |
3D | Aswendt-Lab/AIDAmri | ARA/AllenBrainAPI-master/findAllenExperiments.m | .m | 2,762 | 103 | function varargout = findAllenExperiments(varargin)
% find all Allen experiments defined parameters
%
% function [IDs,json]=findAllenExperiments('param1','val1','param2','val2',...)
%
%
% Inputs
% 'injection' - search for experiments with injections in this location. not searched for by default.
% this i... | MATLAB |
3D | Aswendt-Lab/AIDAmri | ARA/AllenBrainAPI-master/name2structureID.m | .m | 1,653 | 72 | function [IDs,ARA_LIST]=name2structureID(names,ARA_LIST,quiet)
% Convert a list of ARA (Allen Reference Atlas) area names to a vector of structure IDs
%
% function [IDs,ARA_LIST]=name2structureID(names,ARA_LIST,quiet)
%
% Purpose
% Each Allen Reference Atlas (ARA) brain area is associated with a unique
% number (struct... | MATLAB |
3D | Aswendt-Lab/AIDAmri | ARA/AllenBrainAPI-master/structureID2name.m | .m | 2,195 | 83 | function [names,acronyms,ARA_LIST]=structureID2name(structIDs,ARA_LIST,quiet)
% convert a list of ARA (Allen Reference Atlas) structure IDs to a cell array of names
%
% function [names,acronyms,ARA_LIST]=structureID2name(structIDs,ARA_LIST,quiet)
%
% Purpose
% Each Allen Reference Atlas (ARA) brain area is associated w... | MATLAB |
3D | Aswendt-Lab/AIDAmri | ARA/AllenBrainAPI-master/DownloadImageSeries.m | .m | 2,076 | 62 | function DownloadImageSeries(outdir, expid, varargin)
% download Allen sample brain using the Allen API
%
% function DownloadImageSeries(outdir, expid, varargin)
%
%
% Inputs [required]
% outdir - where to put the JPEGs
% expid - [numerical scalar] experiment ID assigned by Allen
%
% Inputs [optional]
% 'downsample' ... | MATLAB |
3D | Aswendt-Lab/AIDAmri | ARA/AllenBrainAPI-master/getProjectionDataFromExperiment.m | .m | 2,762 | 95 | function result = getProjectionDataFromExperiment(expID)
% get projection data from Allen experiment ID
%
% function data = getProjectionDataFromExperiment(expID)
%
% Purpose
% Get projection information from ARA sample brain(s) given one or more experiment IDs.
% These can be searched for using findAllenExperiments
%
... | MATLAB |
3D | Aswendt-Lab/AIDAmri | ARA/AllenBrainAPI-master/acronym2structureID.m | .m | 1,722 | 72 | function [IDs,ARA_LIST]=acronym2structureID(acronyms,ARA_LIST,quiet)
% Convert a list of ARA (Allen Reference Atlas) acronyms to a vector of structure IDs
%
% function [IDs,ARA_LIST]=acronym2structureID(acronyms,ARA_LIST,quiet)
%
% Purpose
% Each Allen Reference Atlas (ARA) brain area is associated with a unique
% numb... | MATLAB |
3D | Aswendt-Lab/AIDAmri | ARA/AllenBrainAPI-master/getInjectionIDfromExperiment.m | .m | 2,188 | 71 | function [IDs,names] = getInjectionIDfromExperiment(expIDs)
% Download structure ID of the primary injection structure from an Allen experiment
%
% function IDs = getInjectionIDfromExperiment(expIDs)
%
% Purpose
% Make an API query that downloads the structure id of the primary injection
% structure of each experime... | MATLAB |
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