SimNIBS to Cifti space Nextflow pipeline

Perform surface mapping from SimNIBS native surface outputs to HCP fs_LR32k space.

Requirements:

• Install Nextflow
• Have singularity containers listed in parameters.json available
  • Note that the connectome workbench container must also have freesurfer available
  • You may use the same container more than once if it contains the appropriate software
• If not in Kimel Lab - add a profile in config/base.nf.config for your cluster setup. If you are not using a cluster you can specify -profile local to run locally on your computer. The profiles available by default are: ['kimel', 'scc', 'local']

Pipelines

• pipeline/mni_transform.nf - perform SimNIBS Freesurfer to MNI brain transformation
• pipeline/simulate_mni.nf - perform SimNIBS simulation using MNI coordinates. Automates registration, coordinate mapping, coil placement, and cifti transformation
• pipeline/simnibs_dscalar.nf - convert SimNIBS outputs to CIFTI format. subject_overlays/ must be available for each subject. You can generate these using map_to_surf when running a SimNIBS simulation

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NOTE: For all pipeline scripts you must run as follows:

nextflow run pipeline/<pipeline>.nf -c <repo_dir>/config/base.nf.config \
	-params-file <repo_dir>/parameters.json [other args...]

• -c - provides base configuration, in addition to the supported profiles
• -params-file - provides list of singularity containers to use

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Example usages

Run simulation using MNI coordinates and obtain CIFTI files

nextflow run pipeline/simulate_mni.nf \
	-c config/base.nf.config -params-file parameters.json \
	--out_dir path/to/out \
	--mri2mesh_dir path/to/mri2mesh/outputs \
	--mni_coordinates 30,43,23 --twist 155 \
	--coil /path/to/coil \
	--create_cifti -profile local

Help

nextflow run pipeline/[mni_transform.nf|simnibs_dscalar.nf|simulate_mni.nf] \
	-c config/base.nf.config \
	--help