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Spinal cord MRI template

Framework for creating MRI templates of the spinal cord. The framework has two distinct pipelines, which has to be run sequentially: Data preprocessing and Template creation.

Important The framework has to be run independently for each contrast. In the end, the generated templates across contrasts should be perfectly aligned. This is what was done for the PAM50 template.

Dependencies

Spinal Cord Toolbox (SCT)

Installation instructions can be found here. For the following repository, we used SCT in developper mode (commit 49a40673e6d1521eb7c2d1d6d7b338ab6811448d).

ANIMAL registration framework

ANIMAL, part of the IPL longitudinal pipeline, is used for generating the template, using iterative nonlinear deformation. The recommanded pipeline for generating a template of the spinal cord is the nonlinear symmetrical template model.

Installation:

git clone https://github.com/vfonov/nist_mni_pipelines.git

Add the following lines to you ~/.bashrc (change the path):

export PYTHONPATH="${PYTHONPATH}:PATH_TO_NIST_MNI_PIPELINES"
export PYTHONPATH="${PYTHONPATH}:PATH_TO_NIST_MNI_PIPELINES/"
export PYTHONPATH="${PYTHONPATH}:PATH_TO_NIST_MNI_PIPELINES/ipl/"
export PYTHONPATH="${PYTHONPATH}:PATH_TO_NIST_MNI_PIPELINES/ipl"

Minc Toolkit v2

The Minc Toolkit is a dependency of the template generation process.

You will also need to install scoop with: pip install scoop

On macOs, you may need to recompile Minc Toolkit from source to make sure all libraires are linked correctly.

On Linux, follow the instructions in the official link above. If you are using Alliance Canada, simply run: module load minc-toolkit/1.9.18

minc2_simple

Install this python library in SCT python.

Dataset structure

The dataset should be arranged according to the BIDS convention. Using the two examples subjects listed in the configuration.json template file, this would be as follows:

dataset/
└── dataset_description.json
└── participants.tsv  <-------------------------------- Metadata describing subjects attributes e.g. sex, age, etc.
└── sub-01  <------------------------------------------ Folder enclosing data for subject 1
└── sub-02
└── sub-03
    └── anat <----------------------------------------- `anat` can be replaced by the value of `data_type` in configuration.json
        └── sub-03_T1w.nii.gz  <----------------------- MRI image in NIfTI format; `_T1w` can be replaced by the value of `suffix_image` in configuration.json
        └── sub-03_T1w.json  <------------------------- Metadata including image parameters, MRI vendor, etc.
        └── sub-03_T2w.nii.gz
        └── sub-03_T2w.json
└── derivatives
    └── labels
        └── sub-03
            └── anat
                └── sub-03_T1w_label-SC_mask.nii.gz  <-- Spinal cord segmentation; `_T1w` can be replaced by the value of `suffix_image` in configuration.json
                └── sub-03_T1w_labels-disc.nii.gz  <---- Disc labels; `_T1w` can be replaced by the value of `suffix_image` in configuration.json
                └── sub-03_T1w_label-centerline.nii.gz  <-- Spinal cord centerline; `_T1w` can be replaced by the value of `suffix_image` in configuration.json
                └── sub-03_T2w_label-SC_mask.nii.gz
                └── sub-03_T2w_labels-disc.nii.gz

Step 1. Data preprocessing

This pipeline includes the following steps:

  1. Install SCT;
  2. Edit configuration file;
  3. Segment spinal cord and vertebral discs;
  4. Quality control (QC) segmentation and labels using SCT's web-based HTML QC report, and download YML files of data to be corrected;
  5. Manually correct files when correction is needed using the SCT manual correction repository;
  6. Copy the non-corrected and corrected files back in the input dataset;
  7. Normalize spinal cord across subjects;
  8. Quality control (QC) spinal cord normalization across subjects.

1.1 Install SCT

SCT is used for all preprocessing steps. The current version of the pipeline uses SCT development version (commit 49a40673e6d1521eb7c2d1d6d7b338ab6811448d) as we prepare for the release of SCT 6.0.

Once SCT is installed, make sure to activate SCT's virtual environment because the pipeline will use SCT's API functions.

source ${SCT_DIR}/python/etc/profile.d/conda.sh
conda activate venv_sct

1.2 Edit configuration file

Copy the file configuration_default.json and rename it as configuration.json. Edit it and modify according to your setup:

  • path_data: Absolute path to the input BIDS dataset; the path should end with /.
  • include_list: List of subjects to include in the preprocessing, separated with a space.
  • data_type: BIDS data type, same as subfolder name in dataset structure. Typically, it should be "anat".
  • contrast: Contrast to be used by sct_deepseg_sc function.
  • suffix_image: Suffix for image data, after subject ID but before file extension (e.g. _rec-composed_T1w in sub-101_rec-composed_T1w.nii.gz).
  • first_disc: Integer value corresponding to the label of the first vertebral disc you want present in the template (see spinalcordtoolbox labeling conventions).
  • last_disc: Integer value corresponding to the label of the last vertebral disc you want present in the template.

Note That SCT functions treat your images with bright CSF as "T2w" (i.e. t2 option) and dark CSF as "T1w" (i.e. t1 option). You can therefore still use SCT even if your images are not actually T1w and T2w.

Note If you wish to make a template that does not align discs across subjects, please open an issue and we will follow-up with you.

1.3 Segment spinal cord and vertebral discs

Run script:

sct_run_batch -script preprocess_segment.sh -config configuration.json -path-output PATH_OUT -jobs N_CPU -script-args configuration.json

Note The value configuration.json should be the same from both the flags -config and -script-args.

With:

  • PATH_OUT: The location where to output the processed data, results, the logs and the QC information. Example: /scratch/template_preproc_YYYYMMDD-HHMMSS. This is a temporary directory in that it is only needed to QC your labels. It therefore cannot be stored inside path_data.
  • N_CPU: The number of CPU cores to dedicate to this task (one subject will be process per core).

1.4 Quality control (QC) labels

  • Spinal cord segmentation (or centerlines) and disc labels can be displayed by opening: PATH_OUT/qc/index.html;
  • Quality control (QC) segmentation and labels using SCT's web-based HTML QC report, and download YML files (qc_fail.yml) of data to be corrected.

1.5 Manual correction

Manually correct files when correction is needed, following the SCT manual correction repository:

  • Installation of manual-correction
  • manual_correction.py script:
python manual_correction.py -path-img PATH_OUT/data_processed -suffix-files-seg '_label-SC_mask' -suffix-files-label '_labels-disc' -config path/to/qc_fail.yml
  • copy_files_to_derivatives.py script:
python copy_files_to_derivatives.py -path-in PATH_OUT/data_processed/derivatives/labels -path-out PATH_DATA/derivatives/labels

Note

  • PATH_DATA: from configuration.json absolute path to the input BIDS dataset.
  • PATH_OUT: The location where to output the processed data, results, the logs and the QC information. Example: /scratch/template_preproc_YYYYMMDD-HHMMSS. Used in Step 1.3.

Note See tutorial for tips on how to QC and fix segmentation (or centerline) and/or disc labels manually.

1.6 Normalize spinal cord across subjects

preprocess_normalize.py contains several functions to normalize the spinal cord across subjects, in preparation for template generation. More specifically:

  • Extracting the spinal cord centerline and computing the vertebral distribution along the spinal cord, for all subjects.
  • Computing the average centerline, by averaging the position of each intervertebral discs.
  • Straightening the average centerline of the spinal cord.
  • Generating the initial template space, based on the average centerline and positions of intervertebral discs,
  • Straightening of all subjects' spinal cord on the initial template space.

Run:

python preprocess_normalize.py configuration.json

1.7 QC of spinal cord normalization

One the preprocessing is performed, please check your data. The preprocessing results should be a series of straight images registered in the same space, with all the vertebral levels aligned with each others.

Step 2. Template creation

Dependencies for template generation (see dependencies)

Now, you can generate the template using the IPL pipeline with the following command, where N has to be replace by the number of subjects:

python -m scoop -n N -vvv generate_template.py

Setting up on Canada's Alliance CPU cluster to generate template

It is recommended to run the template generation on a large cluster. If you are in Canada, you could make use of the Alliance (formerly Compute Canada), which is a bunch of CPU nodes accessible to researchers in Canada. Once the preprocessing is complete, you will generate the template with generate_template.py. This will require minctoolkit v2, minc2simple and nist-mni-pipelines. The easiest way to set up is to use Compute Canada and set up your virtual environment (without spinal cord toolbox, since your data should have already been preprocessed by now) as follows:

a) Copy the dataset folder from your local machine to the cluster You can either drag and drop the folder from your local machine to the cluster, or use the following command:

scp PATH_TO_FOLDER_LOCAL USERNAME@CLUSTER_NAME.computecanada.ca:PATH_TO_FOLDER_CLUSTER

b) Create a virtual environment

module load python
virtualenv --no-download ~/template_env
source ~/template_env/bin/activate

c) Load the right modules and install packages from pip wheel

module load StdEnv/2020  gcc/9.3.0 minc-toolkit/1.9.18.1 python/3.8.10
pip install --upgrade pip
pip install scoop

d) Set up NIST-MNI pipelines

git clone https://github.com/neuropoly/template.git
cd template
git clone https://github.com/vfonov/nist_mni_pipelines.git
NOTE: Current git commit SHA of nist_mni_pipelines used for this version: cadc7219e79d6edb90742e1e340f8eee76332006
nano ~/.bashrc

add the following:

export PYTHONPATH="${PYTHONPATH}:PATH_TO_NIST_MNI_PIPELINES"
export PYTHONPATH="${PYTHONPATH}:PATH_TO_NIST_MNI_PIPELINES/"
export PYTHONPATH="${PYTHONPATH}:PATH_TO_NIST_MNI_PIPELINES/ipl/"
export PYTHONPATH="${PYTHONPATH}:PATH_TO_NIST_MNI_PIPELINES/ipl"

source ~/.bashrc

e) Minc2simple

pip install "git+https://github.com/NIST-MNI/minc2-simple.git@develop_new_build#subdirectory=python"

f) Set environment variable VOLUME_CACHE_THRESHOLD to a value that's smaller then the volume size that you are using in template building

export VOLUME_CACHE_THRESHOLD=-1

g) Update the absolute path of the subjects.csv in the generate_template.py script. The subjects.csv lies inside the DATASET/derivatives/template directory

h) Create template_pipleline.sh

Note: Create the template_pipeline.sh inside the template folder.

#!/bin/bash
python -m scoop -vvv generate_template.py

i) Batch on Alliance Canada

sbatch --time=24:00:00  --mem-per-cpu 4000 template_pipeline.sh # will probably require batching several times, depending on number of subjects

j) Final output

After the pipeline has finished running, the `.mnc` file needs to be converted to `.nii` format in order to get the final template. The pipeline would give outputs with the name: avg.XXX.mnc, where `XXX` is the nth iteration. To convert it to the `.nii` format, run the following command:

mnc2nii PATH_TO/avg.XXX.mnc PATH_TO/template_XXX.nii

Additional information

To have the generated template registered to an existing space (eg, ICBM152), please open an issue and we will follow-up with you.

Licence

This repository is under a MIT licence.