Sulci recognition with Deep CNN

Description

Process to label a new graph using a 3D U-Net convolutional neural network.

The process can work using a GPU or on CPU. It requires a fair amount of RAM memory (about 4-5 GB). If not enough memory can be allocated, the process will abort with an error (thus will not hang the whole machine).

Parameters

graph: Any Type ( input )

input graph to segment

roots: Cortex Catchment Bassins ( input )

root file corresponding to the input graph

model_file: Any Type ( input )

file (.mdsm) storing neural network parameters

param_file: Any Type ( input )

file (.json) storing the hyperparameters (cutting threshold)

rebuild_attributes: Boolean ( input )

skeleton: Cortex Skeleton ( input )

skeleton file corresponding to the input graph

allow_multithreading: Boolean ( input )

labeled_graph: Any Type ( output )

output labeled graph

cuda: Integer ( input )

device on which to run the training(-1 for cpu, i>=0 for the i-th gpu)

fix_random_seed: Boolean ( input )

Use same random sequence

use_capsul_completion: Boolean ( input )

edit_pipeline: Boolean ( input )

capsul_gui: Boolean ( input )

edit_study_config: Boolean ( input )

Technical information

Toolbox : Morphologist

User level : 0

Identifier : sulci_deep_labeling

File name : brainvisa/toolboxes/morphologist/processes/Sulci/Recognition/sulci_deep_labeling.py

Supported file formats :

graph :

Graph, Graph, Graph and data

roots :

gz compressed NIFTI-1 image, Aperio svs, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIF image, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, VIDA image, Ventana bif, XBM image, XPM image, Zeiss czi, gz compressed MINC image, gz compressed NIFTI-1 image

model_file :

mdsm file, mdsm file

param_file :

JSON file, JSON file

skeleton :

gz compressed NIFTI-1 image, Aperio svs, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIF image, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, VIDA image, Ventana bif, XBM image, XPM image, Zeiss czi, gz compressed MINC image, gz compressed NIFTI-1 image

labeled_graph :

Graph, Graph, Graph and data