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CoRNN Diffusion T1 tractography

Enhancing clinically-feasible diffusion MRI tractography utilizing T1w-MRI and anatomical data

Overview

This repository contains the model weights, source code, and containerized implementation of convolutional-recurrent neural network (CoRNN) tractography on low resolution diffusion MRI and T1w MRI with associated SLANT and WM learning (WML) TractSeg segmentations.

Authors and Reference

TBD

Containerization of Source Code

git clone https://github.com/yoonjongyeon/CoRNN_DT1_tractography.git
cd /path/to/repo/CoRNN_DT1_tractography
sudo singularity build /path/to/CoRNN_DT1.sif Singularity

Alternatively, a pre-built container can be downloaded here.

Preparation

Before running a container, output from SLANT and WM learning (WML) TractSeg segmentations are essential.

Command

singularity run 
-e 
--contain
--home <in_dir>
-B <out_dir>:/data
-B <t1_file>:/data/T1.nii.gz
-B <dmri_file>:/data/dmri.nii.gz
-B <bvec_file>:/data/dmri.bvec
-B <bval_file>:/data/dmri.bval
-B <slant_file>:/data/slant/T1_slant.nii.gz
-B <wml_dir>:/data/wml
-B /tmp:/tmp
--nv
/path/to/CoRNN_DT1.sif
/data/T1.nii.gz
/data/dmri.nii.gz
/data/dmri.bvec
/data/dmri.bval
/data/<out_name>
--slant /data/slant/T1_slant.nii.gz
--wml /data/wml
[options]
  • Binding /tmp is required with --contain when --work_dir is not specified.
  • --nv is optional. See --device.

Arguments and I/O

  • <in_dir> Path on the host machine to the directory in which will be used as home directory.

  • <out_dir> Path on the host machine to the directory in which the output tractogram will be saved.

  • <t1_file> Path on the host machine to the T1-weighted MRI with which tractography is to be performed in NIFTI format (either compressed or not).

  • <dmri_file> Path on the host machine to the diffusion MRI with which tractography is to be performed in NIFTI format (either compressed or not).

  • <bvec_file> Path on the host machine to the b-vector file.

  • <bval_file> Path on the host machine to the b-value file.

  • <slant_file> Path on the host machine to the SLANT output file.

  • <wml_dir> Path on the host machine to the TractSeg WM Learning output directory.

  • <out_name> Name (i.e., no directory) of the output tractogram with extension in trk, tck, vtk, fib, or dpy format.

Options

  • --help Print help statement.

  • --device cuda/cpu A string indicating the device on which to perform inference. If "cuda" is selected, container option --nv must be included. Default = "cpu"

  • --num_streamlines N A positive integer indicating the number of streamlines to identify. Default = 1000000

  • --num_seeds N A positive integer indicating the number of streamlines to seed per batch. One GB of GPU memory can handle approximately 10000 seeds. Default = 100000

  • --min_steps N A positive integer indicating the minimum number of 1mm steps per streamline. Default = 50

  • --max_steps N A positive integer indicating the maximum number of 1mm steps per streamline. Default = 250

  • --buffer_steps N A positive integer indicating the number of 1mm steps where the angle stopping criteria are ignored at the beginning of tracking. Default = 5

  • --unidirectional A flag indicating that bidirectional tracking should not be performed. The buffer steps are NOT removed in this case. Default = Perform bidirectional tracking

  • --work_dir /data/work_dir A string indicating the working directory to use. The location of the working directory on the host machine, <work_dir>, must also exist and be bound into the container with -B <work_dir>:/data/work_dir in the command. If the working directory contains previously generated intermediates, the corresponding steps will not be rerun. Default = create a new working directory in /tmp

  • --keep_work A flag indicating that the intermediates in the working directory should NOT be cleared. Default = Clear working directory after completion

  • --num_threads N A positive integer indicating the number of threads to use during multithreaded steps. Default = 1

  • --force A flag indicating that the output file should be overwritten if it already exists. Default = Do NOT override existing output file