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config_neuronal_density_rt.ini
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config_neuronal_density_rt.ini
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# This file makes part of DEEP HISTO
#
# Deep Histo is a medical imaging project that uses deep learning to
# predict histological features from MRI.
#
# Author: Diego Cantor
#------------------------------------------------------------------------------------------------------
# All the files generated by DeepHisto will live inside this directory
#------------------------------------------------------------------------------------------------------
[root]
ROOT : /home/dcantor/projects/deephisto/neuronal_density
#------------------------------------------------------------------------------------------------------
# Study properties
#------------------------------------------------------------------------------------------------------
[study]
name : NEURONAL DENSITY
subjects : 27, 31, 32, 33, 34, 36, 37, 40, 41, 44, 45, 46
#------------------------------------------------------------------------------------------------------
# Where to find the remote files
#------------------------------------------------------------------------------------------------------
[remote files]
remote_ex_vivo_dir :/home/dcantor/remote/epilepsy/{subject}/Processed/Ex-Hist_Reg/9.4T/Neo/aligned_Ex_100um/
remote_histo_dir :/home/dcantor/remote/histology/Histology/{subject}/100um_5umPad_FeatureMaps/aligned/Neo_NEUN/
fa :${remote_ex_vivo_dir}/dti_smoothed_0.2/dti_FA.100um.nii.gz
md :${remote_ex_vivo_dir}/dti_smoothed_0.2/dti_MD.100um.nii.gz
mr :${remote_ex_vivo_dir}/reg_ex_mri_100um.nii.gz
hi :${remote_histo_dir}/count_deformable_100um.nii.gz
#------------------------------------------------------------------------------------------------------
# Where to copy the remote files in the local system
#------------------------------------------------------------------------------------------------------
[local files]
local_exvivo_dir : ${root:ROOT}/subjects/{subject}/exvivo
local_histo_dir : ${root:ROOT}/subjects/{subject}/hist
fa : ${local_exvivo_dir}/dti_FA.100um.nii.gz
md : ${local_exvivo_dir}/dti_MD.100um.nii.gz
mr : ${local_exvivo_dir}/reg_ex_mri_100um.nii.gz
hi : ${local_histo_dir}/count_deformable_100um.nii.gz
#------------------------------------------------------------------------------------------------------
# Settings for PNG file manipulation
#------------------------------------------------------------------------------------------------------
[png]
images_dir : ${root:ROOT}/subjects/{subject}/png
mask_dir : ${root:ROOT}/subjects/{subject}/mask
annotations_dir : ${root:ROOT}/subjects/{subject}/annotations
# Template for the source PNGs
source_png : ${images_dir}/S_{type}_{index}.png
# Template for the histology png
histo_png : ${images_dir}/H_{index}.png
# Template for the labels png
labels_png : ${images_dir}/L_{index}.png
# Template for the annotations zip file
annotations_zip : ${annotations_dir}/{subject}.zip
#slice mask template
slice_mask_png : ${mask_dir}/A_H_{index}.png
#------------------------------------------------------------------------------------------------------
# Visualizer settings
#------------------------------------------------------------------------------------------------------
[visualizer]
#window size (only for visualization, not used for patch window size
wsize : 28
#gist_ncar, nipy_spectral
colormap : jet
#------------------------------------------------------------------------------------------------------
# Patch settings
#------------------------------------------------------------------------------------------------------
[patches]
name : 28x28
patch_size : 28
patch_dir : ${root:ROOT}/patches/${name}
patch_template : ${patch_dir}/{type}_{subject}_{index}_{x}_{y}.png
#------------------------------------------------------------------------------------------------------
# Histology properties
#------------------------------------------------------------------------------------------------------
[histology]
range_min : 0
range_max : 8
#------------------------------------------------------------------------------------------------------
# Classification parameters
#------------------------------------------------------------------------------------------------------
[classification]
num_labels : 10
gaussian_blur : yes
gaussian_radius : 1.5
training_percentage : 0.75
dataset_dir : ${root:ROOT}/dataset/${patches:name}
training_patches : ${dataset_dir}/training.txt
validation_patches : ${dataset_dir}/validation.txt
training_avg_image : ${dataset_dir}/training_average.png
training_avg_value : ${dataset_dir}/training_avg_value.txt
#------------------------------------------------------------------------------------------------------
# Caffe network settings
#------------------------------------------------------------------------------------------------------
[network]
name : nd_rt
network_dir : ${root:ROOT}/caffe/net/${network:name}
network_weights : ${root:ROOT}/caffe/data/${network:name}
training_proto : ${network:network_dir}/training.prototxt
validation_proto : ${network:network_dir}/validation.prototxt
deploy_proto : ${network:network_dir}/deploy.prototxt
random_training : yes
include_rotations : no