Added spinal cord analysis pipeline (Nextflow)

USAGE-ANAT

@@ -0,0 +1,157 @@
+qMRflow mt_sat pipeline
+https://qmrlab.org
+===================
+
+USAGE
+
+nextflow run mtsatflow_BIDS.nf [OPTIONAL_ARGUMENTS] (--root)
+
+DESCRIPTION
+
+    --root=/path/to/[root]              Root folder containing multiple subjects
+
+FOLDER ORGANIZATION
+
+BIDS convention                         For mtsatflow_BIDS.nf
+
+                                        [root]
+                                        ├── sub-01
+                                        │   │── anat
+                                        │   │   ├── sub-01_acq-MTon_MTS.nii.gz
+                                        |   |   ├── sub-01_acq-MTon_MTS.json
+                                        │   │   ├── sub-01_acq-MToff_MTS.nii.gz
+                                        │   │   ├── sub-01_acq-MToff_MTS.json
+                                        │   │   ├── sub-01_acq-T1w_MTS.nii.gz                           
+                                        │   │   └── sub-01_acq-T1w_MTS.json
+                                        │   └── fmap
+                                        │       └── sub-01_B1plusmap.nii.gz (optional)
+                                        └── sub-02
+                                            │── anat
+                                            │   ├── sub-02_acq-MTon_MTS.nii.gz
+                                            |   ├── sub-02_acq-MTon_MTS.json
+                                            │   ├── sub-02_acq-MToff_MTS.nii.gz
+                                            │   ├── sub-02_acq-MToff_MTS.json
+                                            │   ├── sub-02_acq-T1w_MTS.nii.gz                           
+                                            │   └── sub-02_acq-T1w_MTS.json
+                                            └── fmap
+                                                └── sub-02_B1plusmap.nii.gz (optional)
+
+OPTIONAL ARGUMENTS
+
+--platform                      ["octave"/"matlab"] Platform choice. 
+--qmrlab_dir                    ["/path/to/qMRLab" OR null] Absolute path to the qMRLab's 
+                                root directory. If docker is enabled, MUST be set 
+                                to null (without double quotes). If docker is NOT enabled,
+                                then the absolute path to the qMRLab MUST be provided.
+                                Note that qMRLab version MUST be equal or greater than v2.3.1. 
+--octave_path                   ["/path/to/octave_exec" OR null] Absolute path to Octave's 
+                                executable. If docker is enabled, or, if you'd like to use
+                                Octave executable saved to your system path, MUST be set to
+                                null (without double quotes).
+--matlab_path                   ["/path/to/matlab_exec" OR null] Absolute path to MATLAB's 
+                                executable. If you'd like to use MATLAB executable saved to 
+                                your system path, MUST be set to null (without double quotes).
+                                Note that qMRLab requires MATLAB > R2014b. Docker image 
+                                containing MCR compiled version of this application is NOT 
+                                available yet. Therefore, container declerations for the
+                                processes starting with Fit_ prefix MUST be set to null 
+                                (without double quotes).  
+--ants_dim                      [2/3/4] This option forces the image to be treated 
+                                as a specified-dimensional image. If not specified,
+                                ANTs tries to infer the dimensionality.
+--ants_metric                   ["MI"] Confined to MI: Mutual information, for this 
+                                particular pipeline.
+--ants_metric_weight            [0-1] If multimodal (i.e. changing contrast) use weight 1.
+                                This parameter is used to modulate the per stagehting
+                                of the metrics.
+--ants_metric_bins              [e.g. 32] Number of bins.
+--ants_metric_sampling          ["Regular","Random:]The point set can be on a regular 
+                                lattice or a random lattice of points slightly perturbed
+                                to minimize aliasing artifacts.
+--ants_metric_samplingprct      [0-100] The fraction of points to select from the domain
+--ants_transform                "Rigid"
+                                "Affine"
+                                "CompositeAffine"
+                                "Similarity"
+                                "Translation"
+                                "BSpline"
+--ants_convergence              [MxNxO,<convergenceThreshold=1e-6>,<convergenceWindowSize=10>]
+                                Convergence is determined from the number of iterations per level
+                                and is determined by fitting a line to the normalized energy 
+                                profile of the last N iterations (where N is specified by the window
+                                size) and determining the slope which is then compared with the convergence threshold.
+--ants_shrink                   [MxNxO] Specify the shrink factor for the virtual domain (typically 
+                                the fixed image) at each level.
+--ants_smoothing                [MxNxO] Specify the sigma of gaussian smoothing at each level.
+                                Units are given in terms of voxels ('vox') or physical spacing ('mm'). 
+                                Example usage is '4x2x1mm' and '4x2x1vox' where no units implies voxel spacing.
+--use_b1cor                     [true/false] Use and RF transmit field to correct for flip 
+                                angle imperfections. 
+--b1cor_factor                  [0-1] Correction factor (empirical) for the transmit RF. Only
+                                corrects MTSAT, not T1. Default 0.4. 
+--use_bet                       Use FSL's BET for skull stripping.
+--bet_recursive                 [true/false] This option runs more "robust" brain center estimation.
+--bet_threshold                 [0-1] Fractional intensity threshold (0->1); default=0.45; 
+                                smaller values give larger brain outline estimates
+
+
+NOTES
+
+- BIDS:
+
+    mtsatflow_BIDS.nf           To process BIDSified MTsat data. Note that BIDS for 
+                                quantitative MRI data is under development as of 
+                                early 2020. You can visit the GitHub project page
+                                [here](https://github.com/bids-standard/bep001). 
+- Example datasets: 
+
+    Custom-organized data       TBA
+    BIDSified MTsat data        https://osf.io/k4bs5/                                
+
+- Files should be compressed Nifti files (.nii.gz)
+
+- Timing parameters in the .json files MUST be in seconds. 
+
+- Subject IDs are used as the primary process ID and tag throughout the pipeline. 
+
+- We adhere to a strict one-process one-container mapping, where possible using off-the shelf
+  qMRLab containers. 
+
+- All the OPTIONAL ARGUMENTS can be modified in the `nextflow.config` file. The same 
+  config file is consumed by both `mtsatflow.nf` and `mtsatflow_BIDS.nf`.  
+
+- Unless the docker option is enabled in the `nextflow.config`, the following
+  dependencies must be installed and added to the system path: 
+    * ANTs registration (https://github.com/ANTsX/ANTs)
+    * FSL (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/)
+    * Octave/MATLAB (https://www.gnu.org/software/octave/)
+                    (https://www.mathworks.com/)    
+    * qMRLab > v2.3.1       (https://qmrlab.org)
+    * git
+
+If you have Docker installed, enabling docker option will make use of the 
+following Docker images to execute processes: 
+    - qmrlab/minimal (https://hub.docker.com/repository/docker/qmrlab/minimal)
+                      594MB extends to 1.5GB
+                      Built at each qMRLab release.   
+    - qmrlab/antsfsl (https://hub.docker.com/repository/docker/qmrlab/antsfsl)
+                      374MB extends to 1.2GB                      
+                      Dockerfile is available at qMRLab/qMRflow.
+
+- You can take advantage of Nextflow's comprehensive tracing and visualization 
+  features while executing this pipeline: https://www.nextflow.io/docs/latest/tracing.html. 
+
+- For any requests, questions or contributions, please feel free to open
+  an issue at qMRflow's GitHub repo at https://github.com/qMRLab/qMRflow. 
+
+REFERENCES
+
+Please cite the following if you use this module:
+
+    Helms, G. et al. 2008. High-resolution maps of magnetization transfer with inherent correction 
+    for RF inhomogeneity and T1 relaxation obtained from 3D FLASH MRI. Magn. Reson. Med. 60, 1396?1407.
+
+In addition to: 
+
+    Karakuzu A. et al. 2019 The qMRLab workflow: From acquisition to publication., ISMRM 27th Annual
+    Meeting and Exhibition, Montreal, Canada. 

USAGE-SCT

@@ -0,0 +1,79 @@
+Neuromod spinal cord data processing pipeline
+===================
+
+USAGE
+
+Prototype: 
+----------
+nextflow -C neuromod-process-spinalcord.config run neuromod-process-spinalcord.nf [OPTIONAL_ARGUMENTS] (--bids)
+
+Example:
+---------
+nextflow -C neuromod-process-spinalcord.config -log log_directory/sct.log run neuromod-process-spinalcord.nf --bids /neuromod_bids_dir -w /work_directory -with-report report_spinal.html
+
+DESCRIPTION
+
+    --bids=/path/to/[root]              Root folder containing BIDS data
+    -C                                  Use the specified configuration file overriding any defaults.
+    -log                                Set nextflow log file path
+    -w                                  The working directory. Note that if you delete or move the pipeline 
+                                        work directory, this will prevent to use the resume feature in subsequent 
+                                        runs. Also note that the pipeline work directory is intended to be used as a 
+                                        temporary scratch area. The final workflow outputs are expected to be stored in a 
+                                        different location specified using the publishDir directive.
+    -with-report                        Specifcy a report name (e.g. report.html) for having interactive workflow execution report.
+    -resume                             Pass as the last argument if you'd like to resume a previously cached 
+                                        workflow, which was interrupted previously.
+
+FOLDER ORGANIZATION
+
+BIDS convention                         For MTsat data
+
+                                        [root]
+                                        ├── sub-01
+                                            │── ses-001/anat
+                                            │   ├── sub-01_acq-MTon_bp-spine_MTS.nii.gz
+                                            |   ├── sub-01_acq-MTon_bp-spine_MTS.json
+                                            │   ├── sub-01_acq-MToff_bp-spine_MTS.nii.gz
+                                            │   ├── sub-01_acq-MToff_bp-spine_MTS.json
+                                            │   ├── sub-01_acq-T1w_bp-spine_MTS.nii.gz
+                                            │   └── sub-01_acq-T1w_bp-spine_MTS.json
+                                            └── fmap
+                                                └── sub-01_TB1map.nii.gz (optional)
+
+
+OPTIONAL ARGUMENTS
+
+When passed as an argument during `nextflow run` call, the respective value defined for that parameter 
+in the neuromod-process-spinalcord.config will be overridden.
+
+--sct_parameter                          [/this/that/type] Explanation.
+--sct_another_parameter                  [/this/that/type] Explanation.
+
+
+NOTES
+
+- Timing parameters in the .json files MUST be in seconds. 
+
+- Subject IDs are used as the primary process ID and tag throughout the pipeline. Defined by the
+  following BIDS entities: 
+    - sub
+    - ses
+    - rec
+    - acq (unless reserved for inferring file pairs)
+
+
+
+- All the OPTIONAL ARGUMENTS can be modified in the `nextflow.config` file. The same 
+  config file is consumed by both `mtsatflow.nf` and `mtsatflow_BIDS.nf`.  
+
+- Unless the docker option is enabled in the `nextflow.config`, the following
+  dependencies must be installed and added to the system path: 
+    * SCT 
+
+- You can take advantage of Nextflow's comprehensive tracing and visualization 
+  features while executing this pipeline: https://www.nextflow.io/docs/latest/tracing.html. 
+
+REFERENCES
+
+Please cite the following if you use this module:

modules/spinalcord_mtsat.nf

@@ -0,0 +1,29 @@
+// Enable DSL2 so that this can be imported as a module
+nextflow.enable.dsl=2
+
+/* This PLACEHOLDER process is to explain the relationship 
+between the files emitted by the input channels, process and  
+how those files are process to emit outputs */ 
+
+process MTS_Align_SpinalCord{
+    tag { sid }
+
+    input:
+        tuple val(sid), file(pdw), file(mtw), file(t1w)
+
+    output:
+        tuple val(sid), \
+        path("${sid}_MTSAT_example.txt"), \
+        emit: publish_spinal_mtsat
+
+    script: 
+        """
+        echo "sct_parameter was $params.sct_parameter\n" >> ${sid}_MTSAT_example.txt
+        echo "the other one was $params.sct_another_parameter\n" >> ${sid}_MTSAT_example.txt
+        echo "sid is ${sid}\n" >> ${sid}_MTSAT_example.txt
+        echo "MTon is $mtw\n" >> ${sid}_MTSAT_example.txt
+        echo "MToff is $pdw\n" >> ${sid}_MTSAT_example.txt
+        echo "T1w is $t1w\n" >> ${sid}_MTSAT_example.txt
+        echo "ENV vars can be captured: $PATH\n" >> ${sid}_MTSAT_example.txt
+        """
+}

modules/spinalcord_segmentation.nf

@@ -0,0 +1,43 @@
+// Enable DSL2 so that this can be imported as a module
+nextflow.enable.dsl=2
+
+/* This PLACEHOLDER process is to explain the relationship 
+between the files emitted by the input channels, process and  
+how those files are process to emit outputs */ 
+
+// TODO: find a way to avoid this code duplication below
+process T1_Segment_SpinalCord{
+    tag { sid }
+
+    input:
+        tuple val(sid), file(t2w)
+
+    output:
+        tuple val(sid), \
+        path("${sid}_bp-cspine_T1w_seg.nii.gz"), \
+        emit: publish_spinalcord
+
+    script: 
+        """
+        sct_deepseg_sc -i $t2w -c t1 -qc $params.qcDir -qc-subject ${sid}
+        """
+
+}
+
+process T2_Segment_SpinalCord{
+    tag { sid }
+
+    input:
+        tuple val(sid), file(t2w)
+
+    output:
+        tuple val(sid), \
+        path("${sid}_bp-cspine_T2w_seg.nii.gz"), \
+        emit: publish_spinal_seg
+
+    script: 
+        """
+        sct_deepseg_sc -i $t2w -c t2 -qc $params.qcDir -qc-subject ${sid}
+        """
+
+}

neuromod-process-spinalcord.config

@@ -0,0 +1,41 @@
+//** Official documentation for config files: https://www.nextflow.io/docs/latest/config.html **//
+
+process {
+
+    withName: SpinalCord {
+        cpus = 4
+        memory = 4.GB
+        maxForks = 2
+    }
+
+}
+
+params {
+
+    sct_parameter= "This is how default params are defined"
+    sct_another_parameter= 99
+    qcDir = "$params.bids/derivatives/SCT/qc"
+
+}
+
+//** Default one is standard (local), but other options are easily possible **//
+
+profiles {
+
+    standard {
+        process.executor = 'local'
+    }
+
+    cluster {
+        process.executor = 'slurm'
+        process.queue = 'long'
+        process.memory = '10GB'
+    }
+
+    cloud {
+        process.executor = 'awsbatch'
+        process.container = 'docker.io/neuropoly/sct'
+        docker.enabled = true
+    }
+
+}