MCRIBS

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Surface version of the M-CRIB atlases.

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# M-CRIB-S
Surface version of M-CRIB.

This software uses ANTs/antsJointFusion for voxel labeling and Deformable within MIRTK to perform cortical surface extraction.
A customised Freesurfer-like pipeline is provided to perform cortical parcellation on the surfaces with M-CRIB compatible labelling schemes.

The paper is available at https://www.nature.com/articles/s41598-020-61326-2

MIRTK was downloaded from https://github.com/BioMedIA/MIRTK. A customised version is included in this repo.

# Installation

Check the source code out by

```
git checkout https://github.com/DevelopmentalImagingMCRI/MCRIBS.git
cd MCRIBS
./build.sh
```

The script build.sh will build ITK, VTK and MIRTK. Install the following dependencies prior to running:

- For VTK
  - zlib1g-dev libboost-dev libglu1-mesa-dev libxt-dev python3-dev libeigen3-dev
- For MIRTK
  - libtbb-dev libflann-dev python-contextlib2
- For Python
  - python3-contextlib2 python3-contextlib2 python3-imageio python3-numpy python3-scipy python3-pandas python3-numexpr

This will install all of the dependencies for ubuntu:

`apt install zlib1g-dev libboost-dev libglu1-mesa-dev libxt-dev python-dev python3-dev libtbb-dev libflann-dev libeigen3-dev python-contextlib2 python3-contextlib2 python3-imageio python3-numpy python3-scipy python3-pandas python3-numexpr`

In centos, do this:

`yum install zlib-devel boost-devel mesa-libGLU-devel libXt-devel python-devel python3-devel tbb-devel eigen3-devel python-contextlib2 python3-contextlib2 python3-imageio python3-numpy python3-scipy python3-pandas python3-numexpr`

The script build.sh will checkout VTK 9.3, ITK 5.3 and build it.

## Docker version

Pull the latest docker image from Docker Hub with the command:

```
docker pull developmentalimagingmcri/mcribs:latest
```

Run the software using the following command:

```
docker run \
  --rm \
  -it \
  --mount type=bind,source=<work dir>,target=/work \
  --mount type=bind,source=<freesurfer license>,target=/opt/freesurfer-license.txt \
  developmentalimagingmcri/mcribs:latest MCRIBReconAll ...
```

Where

- *work dir*: is the location of your base directory on the host, to be explained later.
- *freesurfer license*: is the location of the Freesurfer 7 license file on the host machine.

# Set up script

Depending on the shell you are using source the configuration files as follows:

- Bash: `. MCRIBS/SetUpMCRIBS.sh`
- TCSH shell: `source MCRIBS/SetUpMCRIBS.csh`

The main script to run is MCRIBReconAll. To get usage run MCRIBReconAll --help

## Set up your data

Place your raw structural images, for subject `subjid` into subdirectories as follows:

* T2 structural: `RawT2/subjid.nii.gz`
* T1 structural: `RawT1/subjid.nii.gz` (optional)

## Running

There is a wrapper script called `MCRIBReconAll` that runs the pipeline of segmentation, surface extraction. The synopsis of the command is:

`MCRIBReconAll [processing directive] [options] <subject id>`

### Processing directives and options

- --neckcrop: Reorients T2 image to radiological orientation, axial slices, resamples to isotropic voxels. Input <RawT2/subjid.nii.gz> Output <T2NeckCroppedIsotropic/subjid.nii.gz>
  - Options:
  - --voxelsize VOXELSIZE: Voxel size to use for isotropic resampling. Use "volumepreserve" to preserve original voxel volume
- --tissueseg: Tissue type segmentation, depends on --conform. Input <T2NeckCroppedIsotropic/subjid.nii.gz> Outputs <TissueSeg>
  - Options:
  -  --gmsegcompthreshold GMSEGCOMPTHRESHOLD: Threshold for GM segmentation connected components (0, 1]
- --surfrecon: Cortical surface extraction, depends --tissueseg. Inputs <TissueSeg>, Outputs <SurfReconDeformable/subjid>
  - Options:
  - --surfreconmethod {Deformable}: Specify cortical surface extraction method
  - --deformablejointhresh DEFORMABLEJOINTHRESH: Join threshold parameter for Deformable, default=1.
  - --deformablefastcollision: Use Deformable fast collision test
- --inflatesphere: Perform inflation, spherical mapping, curv, area, depends --surfrecon. Inputs <SurfReconDeformable/subjid>, Outputs <freesurfer/subjid>
- --surfreg: Perform surface registration to the spherical template, depends --surfrecon
- --surfvol: Perform surface volume calculations, depends --surfrecon
- --cortribbon: Perform cortical ribbon volume generation, depends --surfrecon
- --cortparc: Perform cortical parcellation, depends on --surfreg
  - Options:
  - --parcatlases {aparc+DKTatlas} [{aparc+DKTatlas} ...]: Parcellation scheme(s) to use
- --aparc2aseg: Transfer cortical parcellations to volume, depends on --surfreg
  - Options:
  - --parcatlases {aparc+DKTatlas} [{aparc+DKTatlas} ...] Parcellation scheme(s) to use
- --cortthickness: Compute cortical thickness
- --segstats: Perform segstats on the aseg image, depends on --apas2aseg
- --parcstats: Perform stats on the cortical surfaces, depends on --apas2aseg

The following shorthand options may be used:

- --all: executes --neckcrop, --tissueseg, --surfrecon, --inflatesphere, --surfreg, --surfvol, --cortribbon, --cortparc, --aparc2aseg, --apas2aseg, --cortthickness, --segstats, --parcstats
- -autoreconaftersurf: executes all steps post surface extraction, i.e. --inflatesphere, --surfreg, --surfvol, --cortribbon, --cortparc, --aparc2aseg, --apas2aseg, --cortthickness, --segstats, --parcstats

Other options:
- -openmp, --openmp nthreads. Use nthreads for multithreading where possible.

MCRIBS

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