GitHub - frankfan007/mcgeometry: Monte Carlo-based geometry-driven toolbox to fit diffuse correlation spectroscopy data

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 21 Commits
mc		mc
mri		mri
raw		raw
results		results
sample		sample
volumes		volumes
LICENSE.txt		LICENSE.txt
ProgressBar.m		ProgressBar.m
README.txt		README.txt
TODO.txt		TODO.txt
alphavol.m		alphavol.m
analytical_fit_dcs.m		analytical_fit_dcs.m
concatenate_layers.m		concatenate_layers.m
find_subplot_dims.m		find_subplot_dims.m
fit_g2_MC.m		fit_g2_MC.m
generate_bin_vol.m		generate_bin_vol.m
generate_input_file.m		generate_input_file.m
generate_mri_mesh.m		generate_mri_mesh.m
generate_subject_seg.m		generate_subject_seg.m
get_normal_plane_from_point.m		get_normal_plane_from_point.m
get_region_splits.m		get_region_splits.m
i2m_close.m		i2m_close.m
i2m_open.m		i2m_open.m
ismonotonic.m		ismonotonic.m
load_history_file.m		load_history_file.m
loop_and_fit_dcs.m		loop_and_fit_dcs.m
loop_and_fit_dcs_parallel.m		loop_and_fit_dcs_parallel.m
make_stairhead.m		make_stairhead.m
mc_g2_Db_beta_hold_layer.m		mc_g2_Db_beta_hold_layer.m
merge_structures.m		merge_structures.m
parallel_fitdcs_function_multi_combos.m		parallel_fitdcs_function_multi_combos.m
parallel_fitdcs_function_single_combo.m		parallel_fitdcs_function_single_combo.m
plot_analytical_fit_results.m		plot_analytical_fit_results.m
plot_mc_fitting_result.m		plot_mc_fitting_result.m
plot_mesh_layers.m		plot_mesh_layers.m
pre_process_dcs_data.m		pre_process_dcs_data.m
prepare_dcsraw_data.m		prepare_dcsraw_data.m
prepare_fastdcs_data.m		prepare_fastdcs_data.m
prepare_migraine_dcs_data.m		prepare_migraine_dcs_data.m
prepare_sampledcs_data.m		prepare_sampledcs_data.m
print_box.m		print_box.m
print_box_with_height.m		print_box_with_height.m
readDCS.m		readDCS.m
read_single_history_file.m		read_single_history_file.m
return_input_file_status.m		return_input_file_status.m
run_mc_simulation.m		run_mc_simulation.m
semi_infinite_g2.m		semi_infinite_g2.m
set_parameters_for_given_volume.m		set_parameters_for_given_volume.m
wrap_probe.m		wrap_probe.m
write_input_file.m		write_input_file.m

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THIS TOOLBOX IS CURRENTLY BEING DEVELOPED FOR PUBLIC USE AND IS IN PROGRESS

mcgeometry is a Monte-Carlo based fitting toolbox for diffuse correlation spectroscopy data

Operating systems currently supported: Linux

Author:

Melissa Wu
mwu22@mgh.harvard.edu
Athinoula A Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Harvard Medical School

149 13th St
Charlestown, MA 02129

Version: 1.0.0

License: GNU Public License Version 2.0

Required software:

iso2mesh (http://iso2mesh.sf.net)
MCX (for computing systems with GPUs, http://mcx.space/) OR tMCimg (for computing systems without GPUs, http://www.nmr.mgh.harvard.edu/PMI/resources/tmcimg/index.htm)
FreeSurfer (https://surfer.nmr.mgh.harvard.edu/)

**NOTE: I cannot push Monte Carlo photon history files as they exceed the storage limit for Github. Please download MCX or tMCimg to obtain photon history files

Acknowledgement:

This work was supported by US National Institutes of Health grants R01NS100750, R21NS094828, R01EB02514501, and P41EB015896.