Command Line Usage¶
TNT_pipeline_2
usage: TNT_pipeline_2 [-h] [--working_directory WORKING_DIRECTORY]
[--skip_validation]
[--nipype_plugin {Linear,MultiProc,Debug}]
[--n_proc N_PROC] [--memory_gb MEMORY_GB]
[--profiling_output_file PROFILING_OUTPUT_FILE]
[--loglevel {INFO,DEBUG}] [--model_space MODEL_SPACE]
[--subcortical]
[--subcortical_model_space SUBCORTICAL_MODEL_SPACE]
[--intracranial_volume]
[--participant_labels PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
[--model MODEL] [--atlas ATLAS]
[--atlas_labels ATLAS_LABELS] [--tags TAGS]
[--tag_labels TAG_LABELS]
[--model_brain_mask MODEL_BRAIN_MASK]
[--bet_frac BET_FRAC]
[--bet_vertical_gradient BET_VERTICAL_GRADIENT]
[--inormalize_const2 INORMALIZE_CONST2 INORMALIZE_CONST2]
[--inormalize_range INORMALIZE_RANGE] [--debug]
[--debug_io] [--graph_output GRAPH_OUTPUT]
[--filter_session [SESSION]]
[--filter_acquisition [ACQUISITION]]
[--filter_reconstruction [RECONSTRUCTION]]
[--filter_run [RUN]]
[--subcortical_model SUBCORTICAL_MODEL]
[--subcortical_atlas SUBCORTICAL_ATLAS]
[--subcortical_labels SUBCORTICAL_LABELS]
[--subcortical_model_brain_mask SUBCORTICAL_MODEL_BRAIN_MASK]
[--intracranial_mask INTRACRANIAL_MASK]
[--max_shear_angle MAX_SHEAR_ANGLE]
[--resource_input_file RESOURCE_INPUT_FILE]
[--ants_n_proc ANTS_N_PROC]
[--qc_config_file QC_CONFIG_FILE]
[--qc_config_file_out QC_CONFIG_FILE_OUT]
[--profiling_input_file PROFILING_INPUT_FILE]
[--resource_output_file RESOURCE_OUTPUT_FILE]
input_dataset output_folder
{participant,group,qcpages,create_resource_file}
Positional Arguments¶
| input_dataset | Location of BIDS dataset |
| output_folder | Output directory |
| analysis_level | Possible choices: participant, group, qcpages, create_resource_file “participant” runs the main pipeline on each subject independently. “group” consolidates the results. “qcpages” uses PipelineQC to generate QC pages. “create_resource_file” uses profiling data (–profiling_output_file) to create a resource file with processor and memory usage for each node. |
General Arguments¶
Arguments for all analysis levels (except create_resource_file)
| --working_directory | |
| (Passed to the nipype workflow) | |
| --skip_validation | |
Skip bids validation Default: False | |
| --nipype_plugin | |
Possible choices: Linear, MultiProc, Debug Specify the nipype workflow execution plugin. “Linear” will aid debugging. Default: “MultiProc” | |
| --n_proc | The number of processors to use with the MultiProc plugin. If not set determine automatically. |
| --memory_gb | Max memory parameter to use with the MultiProc plugin. If not set determine automatically. |
| --profiling_output_file | |
| If set, set resource monitoring in nipype and save results tothis file (JSON format). | |
| --loglevel | Possible choices: INFO, DEBUG Log level passed to nipype configuration variables workflow_level, utils_level, and interface_level. Default: “INFO” |
Participant and QC pages arguments¶
Arguments for “participant” and “qcpages”
| --model_space | The name of the model space. Used only for naming files. Default: “SYS808” |
| --subcortical | Run subcortical pipeline Default: False |
| --subcortical_model_space | |
The name of the subcortical model space. Only used for naming files. REQUIRED if “–subcortical” is set. Default: “colin” | |
| --intracranial_volume | |
Calculate intracranial volume Default: False | |
Participant Arguments¶
Arguments for participant analysis level
| --participant_labels | |
| Subjects on which to run the pipeline. If not specified, run on all. | |
| --model | A model/template brain in the same space as “–atlas” and “–tags”. Will be registered with T1w images to map template space to native space. Default: $INSTALLDIR/TNT_pipeline_2/data/SYS_808.nii.gz |
| --atlas | Atlas in model/template space subdividing the brain into lobes. This atlas will be transformed to native space and combined with the GM and WM maps. Default: $INSTALLDIR/TNT_pipeline_2/data/SYS808_atlas_labels_nomiddle.nii.gz |
| --atlas_labels | A BIDS style label file (i.e. a tab-separated values file with “index” and “name” columns described in BEP011). Describes the lobes in “atlas”. If not specified will look for a file with the same name ias “–atlas” but ending in “_labels.tsv”. |
| --tags | A TSV file with columns “x”, “y”, “z”, and “index” (float, float, float, int, respectively). these points are used to train the classifier. Note that if both the qform and sform of model are specified, the qform will be used, so the tags must be in those coordinates. Default: $INSTALLDIR/TNT_pipeline_2/data/ntags_1000_prob_90_nobg_sys808.tsv |
| --tag_labels | A label file mapping “index” in “–tags” to tissue names. |
| --model_brain_mask | |
Brain mask in model/template space. Default: $INSTALLDIR/TNT_pipeline_2/data/SYS808_brainmask.nii.gz | |
| --bet_frac | Argument passed to FSL’s BET Default: 0.5 |
| --bet_vertical_gradient | |
Argument passed to FSL’s BET Default: 0.0 | |
| --inormalize_const2 | |
Passed to inormalize –const2 parameter Default: [0.0, 5000.0] | |
| --inormalize_range | |
Passed to inormalize –range parameter Default: 1.0 | |
| --debug | Set ANTs iteration count to 1 to make the workflow fast. Default: False |
| --debug_io | Bypass main workflow to test the input/output logic. Default: False |
| --graph_output | Generate a graph of the workflow and save as “–graph_output”. |
| --filter_session | |
| Use only T1w scans that have session parameter SESSION. If this parameter is set without an argument, only scans which do not have the session parameter will be selected. | |
| --filter_acquisition | |
| Use only T1w scans that have acquisition parameter ACQUISITION. If this parameter is set without an argument, only scans which do not have the acquisition parameter will be selected. | |
| --filter_reconstruction | |
| Use only T1w scans that have reconstruction parameter RECONSTRUCTION. If this parameter is set without an argument, only scans which do not have the reconstruction parameter will be selected. | |
| --filter_run | Use only T1w scans that have run parameter RUN. If this parameter is set without an argument, only scans which do not have the run parameter will be selected. |
| --subcortical_model | |
A model/template in the same space as “–subcortical_atlas”. Will be registered with each subject. REQUIRED if “–subcortical” is set. Default: $INSTALLDIR/TNT_pipeline_2/data/colin27_t1_tal_lin.nii.gz | |
| --subcortical_atlas | |
Atlas in delineating subcortical structures. REQUIRED if “–subcortical” is set. Default: $INSTALLDIR/TNT_pipeline_2/data/mask_oncolinnl_7_rs.nii.gz | |
| --subcortical_labels | |
| A label file mapping the labels in “–subcortical_atlas” to structure names | |
| --subcortical_model_brain_mask | |
Brain mask for subcortical_model. REQUIRED if “–subcortical” is set. Default: $INSTALLDIR/TNT_pipeline_2/data/colin27_t1_tal_lin_mask2.nii.gz | |
| --intracranial_mask | |
Intracranial mask in reference space. REQUIRED if “–intracranial_volume” is set. Default: $INSTALLDIR/TNT_pipeline_2/data/SYS808_icv.nii.gz | |
| --max_shear_angle | |
Input files are pass through forceqform to ensure that only the qform is set. max_shear_angle is the maximum permissible shear in the rotation matrix if only the sform is set. Shear angle is calculated as the the absolute difference between the angles between coordinates and 90 degress. Default: 1e-06 | |
| --resource_input_file | |
| JSON file of node usage. Created using create_resource_file command. This will set the processor count and memory usage for each node based on the profiling run. | |
| --ants_n_proc | Number of processors to use for ANTs tools. Default: 1 |
QC Pages Arguments¶
Arguments for qcpages analysis level
| --qc_config_file | |
| Configuration file passed to PipelineQC. | |
| --qc_config_file_out | |
| Output file name for qc config (JSON) | |
Create resource file arguments¶
Arguments for the create_resource_file analysis level
| --profiling_input_file | |
| Output from –profiling_output_file | |
| --resource_output_file | |
| Resource file to be passed to –resource_input_file | |