Getting Started

Singularity

The easiest way to get started is to install using singularity

singularity build $name docker://pndni/tnt_pipeline_2:$ver

where $name is the name of the saved image, e.g. tnt_pipeline_2.sif, and $ver is the version. See docker hub for which tags are available.

Basic Usage

This assumes you are in a directory with the singularity image tnt_pipeline_2.sif, a bids directory bids, and output directory out. The basic usage is

singularity run --cleanenv --no-home tnt_pipeline_2.sif bids out participant

To include intracranial volume and subcortical structures

singularity run --cleanenv --no-home tnt_pipeline_2.sif bids out participant \
--intracranial_volume \
--subcortical

The default model is SYS808. If a different model is needed, then you’ll need to specify some additional information. For example, to use an MNI model

singularity run --cleanenv --no-home tnt_pipeline_2.sif bids out participant \
--intracranial_volume \
--subcortical \
 --model_space ICBM152NlinSymIV \
 --model models/icbm_avg_152_t1_tal_nlin_symmetric_VI.nii \
 --atlas models/atlas_labels_nomiddle_rs.nii \
 --tags models/ntags_1000_prob_90_nobg.tsv \
 --model_brain_mask models/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.nii \
 --intracranial_mask models/icbm_ICVmask_tp2013.nii

Where --model_space is just a name you choose, --model is the actual model brain, --atlas labels each ROI on the model (e.g., lobes), --tags is a list of points and their classification to train the classifier, --model_brain_mask is a mask of the brain in model space, and --intracranial_mask is used to calculate intracranial volume. This assumes that a file labeling the atlas ROIs named --models/icbm_avg_152_t1_tal_nlin_symmetric_VI_labels.tsv exists and a file labeling the tags named --models/ntags_1000_prob_90_nobg_labels.tsv exists. This can be overridden with --atlas_labels and --tag_labels, respectively. See Command Line Usage for more information.