Getting started
Installation Instructions for Users
User Documentation
Connectome Mapper 3 and the BIDS standard
Commandline Usage
Graphical User Interface
Outputs of Connectome Mapper 3
API Documentation
Packages and modules
Examples & Tutorials
Adopting Datalad for collaboration
Running on a cluster (HPC)
About Connectome Mapper
BSD 3-Clause License
Changes
Citing
Contributing to Connectome Mapper 3
Support, Bugs and New Feature Requests
Connectome Mapper 3
Docs
»
Index
Edit on GitHub
Index
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E
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F
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G
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H
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I
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
A
aggregate_outputs() (cmtklib.interfaces.fsl.Orient method)
anat_available_config (cmp.project.CMP_Project_Info attribute)
anat_config (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
anat_config_error_msg (cmp.project.CMP_Project_Info attribute)
anat_config_error_view (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
anat_config_to_load (cmp.project.CMP_Project_Info attribute)
anat_custom_last_stage (cmp.project.CMP_Project_Info attribute)
anat_flow (cmp.pipelines.common.Pipeline attribute)
anat_inputs_checked (cmp.bidsappmanager.gui.CMP_ConfiguratorWindow attribute)
(cmp.bidsappmanager.gui.CMP_InspectorWindow attribute)
(cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler attribute)
(cmp.bidsappmanager.project.CMP_MainWindowHandler attribute)
anat_load_config_json() (in module cmtklib.config)
anat_outputs_checked (cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler attribute)
(cmp.bidsappmanager.project.CMP_MainWindowHandler attribute)
anat_pipeline (cmp.bidsappmanager.gui.CMP_ConfiguratorWindow attribute)
(cmp.bidsappmanager.gui.CMP_InspectorWindow attribute)
(cmp.bidsappmanager.gui.CMP_MainWindow attribute)
(cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler attribute)
(cmp.bidsappmanager.project.CMP_MainWindowHandler attribute)
anat_run (cmp.project.CMP_Project_Info attribute)
anat_runs (cmp.project.CMP_Project_Info attribute)
anat_save_config (cmp.bidsappmanager.gui.CMP_ConfiguratorWindow attribute)
anat_save_config() (in module cmtklib.config)
anat_select_config_to_load (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
anat_stage_names (cmp.project.CMP_Project_Info attribute)
anat_warning_view (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
anatomical_processed (cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler attribute)
(cmp.bidsappmanager.project.CMP_MainWindowHandler attribute)
AnatomicalPipeline (class in cmp.pipelines.anatomical.anatomical)
AnatomicalPipelineUI (class in cmp.bidsappmanager.pipelines.anatomical.anatomical)
angle (cmp.stages.diffusion.tracking.MRtrix_tracking_config attribute)
ants_bspline_interpolation_parameters (cmp.stages.registration.registration.RegistrationConfig attribute)
ants_convergence_thresh (cmp.stages.registration.registration.RegistrationConfig attribute)
ants_convergence_winsize (cmp.stages.registration.registration.RegistrationConfig attribute)
ants_gauss_interpolation_parameters (cmp.stages.registration.registration.RegistrationConfig attribute)
ants_interpolation (cmp.stages.registration.registration.RegistrationConfig attribute)
ants_linear_cost (cmp.stages.registration.registration.RegistrationConfig attribute)
ants_linear_gradient_step (cmp.stages.registration.registration.RegistrationConfig attribute)
ants_linear_sampling_perc (cmp.stages.registration.registration.RegistrationConfig attribute)
ants_linear_sampling_strategy (cmp.stages.registration.registration.RegistrationConfig attribute)
ants_lower_quantile (cmp.stages.registration.registration.RegistrationConfig attribute)
ants_multilab_interpolation_parameters (cmp.stages.registration.registration.RegistrationConfig attribute)
ants_nonlinear_cost (cmp.stages.registration.registration.RegistrationConfig attribute)
ants_nonlinear_gradient_step (cmp.stages.registration.registration.RegistrationConfig attribute)
ants_nonlinear_total_field_variance (cmp.stages.registration.registration.RegistrationConfig attribute)
ants_nonlinear_update_field_variance (cmp.stages.registration.registration.RegistrationConfig attribute)
ants_perform_syn (cmp.stages.registration.registration.RegistrationConfig attribute)
ants_precision_type (cmp.stages.parcellation.parcellation.ParcellationConfig attribute)
ants_probmaskfile (cmp.stages.segmentation.segmentation.SegmentationConfig attribute)
ants_regmaskfile (cmp.stages.segmentation.segmentation.SegmentationConfig attribute)
ants_templatefile (cmp.stages.segmentation.segmentation.SegmentationConfig attribute)
ants_upper_quantile (cmp.stages.registration.registration.RegistrationConfig attribute)
apply_scrubbing (cmp.stages.connectome.fmri_connectome.ConnectomeConfig attribute)
apply_to_eroded_brain (cmp.stages.registration.registration.RegistrationConfig attribute)
apply_to_eroded_csf (cmp.stages.registration.registration.RegistrationConfig attribute)
apply_to_eroded_wm (cmp.stages.registration.registration.RegistrationConfig attribute)
ApplymultipleMRConvert
ApplymultipleMRCrop
ApplymultipleMRTransforms
ApplymultipleWarp
ApplymultipleXfm
atlas_info (cmp.project.CMP_Project_Info attribute)
(cmp.stages.parcellation.parcellation.ParcellationConfig attribute)
B
backtrack (cmp.stages.diffusion.tracking.MRtrix_tracking_config attribute)
Bandpass
base_directory (cmp.project.CMP_Project_Info attribute)
base_name (cmtklib.diffusion.Make_Mrtrix_Seeds attribute)
(cmtklib.diffusion.Make_Seeds attribute)
BBRegister
BColors (class in cmtklib.util)
bias_field_algo (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute)
bias_field_correction (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute)
bids_dir (cmp.stages.common.Stage attribute)
bids_layout (cmp.project.CMP_Project_Info attribute)
bids_root (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
bidsapp (cmp.bidsappmanager.gui.CMP_MainWindow attribute)
bidsapp_tag (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
bidsapp_ui (cmp.bidsappmanager.gui.CMP_MainWindow attribute)
big_delta (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
BinaryThreshold
BOLD (cmtklib.util.BColors attribute)
brain_mask_extraction_tool (cmp.stages.segmentation.segmentation.SegmentationConfig attribute)
brain_mask_path (cmp.stages.segmentation.segmentation.SegmentationConfig attribute)
C
Camino2Trackvis
check (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
check_config() (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline method)
(cmp.pipelines.common.Pipeline method)
(cmp.pipelines.diffusion.diffusion.DiffusionPipeline method)
(cmp.pipelines.functional.fMRI.fMRIPipeline method)
check_configuration_format() (in module cmtklib.config)
check_configuration_version() (in module cmtklib.config)
check_input() (cmp.bidsappmanager.pipelines.anatomical.anatomical.AnatomicalPipelineUI method)
(cmp.bidsappmanager.pipelines.diffusion.diffusion.DiffusionPipelineUI method)
(cmp.bidsappmanager.pipelines.functional.fMRI.fMRIPipelineUI method)
(cmp.pipelines.anatomical.anatomical.AnatomicalPipeline method)
(cmp.pipelines.diffusion.diffusion.DiffusionPipeline method)
(cmp.pipelines.functional.fMRI.fMRIPipeline method)
Check_Input_Notification (class in cmp.pipelines.anatomical.anatomical)
Check_Input_NotificationUI (class in cmp.bidsappmanager.pipelines.anatomical.anatomical)
check_output() (cmp.bidsappmanager.pipelines.anatomical.anatomical.AnatomicalPipelineUI method)
(cmp.pipelines.anatomical.anatomical.AnatomicalPipeline method)
check_settings() (cmp.bidsappmanager.gui.CMP_BIDSAppWindow method)
(cmp.bidsappmanager.project.CMP_BIDSAppWindowHandler method)
check_stages_execution() (cmp.pipelines.common.Pipeline method)
circular_layout (cmp.bidsappmanager.stages.connectome.connectome.ConnectomeStageUI attribute)
(cmp.bidsappmanager.stages.connectome.fmri_connectome.ConnectomeStageUI attribute)
(cmp.stages.connectome.connectome.ConnectomeConfig attribute)
(cmp.stages.connectome.fmri_connectome.ConnectomeConfig attribute)
clean_cache() (in module cmp.bidsappmanager.project)
clear_stages_outputs() (cmp.pipelines.common.Pipeline method)
cmat() (in module cmtklib.connectome)
cmp
module
,
[1]
cmp.bidsappmanager
module
cmp.bidsappmanager.core
module
cmp.bidsappmanager.gui
module
cmp.bidsappmanager.images
module
cmp.bidsappmanager.pipelines
module
cmp.bidsappmanager.pipelines.anatomical
module
cmp.bidsappmanager.pipelines.anatomical.anatomical
module
cmp.bidsappmanager.pipelines.diffusion
module
cmp.bidsappmanager.pipelines.diffusion.diffusion
module
cmp.bidsappmanager.pipelines.functional
module
cmp.bidsappmanager.pipelines.functional.eeg
module
cmp.bidsappmanager.pipelines.functional.fMRI
module
cmp.bidsappmanager.project
module
cmp.bidsappmanager.stages
module
cmp.bidsappmanager.stages.connectome
module
cmp.bidsappmanager.stages.connectome.connectome
module
cmp.bidsappmanager.stages.connectome.fmri_connectome
module
cmp.bidsappmanager.stages.diffusion
module
cmp.bidsappmanager.stages.diffusion.diffusion
module
cmp.bidsappmanager.stages.diffusion.reconstruction
module
cmp.bidsappmanager.stages.diffusion.tracking
module
cmp.bidsappmanager.stages.functional
module
cmp.bidsappmanager.stages.functional.functionalMRI
module
cmp.bidsappmanager.stages.parcellation
module
cmp.bidsappmanager.stages.parcellation.parcellation
module
cmp.bidsappmanager.stages.preprocessing
module
cmp.bidsappmanager.stages.preprocessing.fmri_preprocessing
module
cmp.bidsappmanager.stages.preprocessing.preprocessing
module
cmp.bidsappmanager.stages.registration
module
cmp.bidsappmanager.stages.registration.registration
module
cmp.bidsappmanager.stages.segmentation
module
cmp.bidsappmanager.stages.segmentation.segmentation
module
cmp.cli
module
cmp.cli.cmpbidsappmanager
module
cmp.cli.connectomemapper3
module
cmp.cli.showmatrix_gpickle
module
cmp.parser
module
cmp.pipelines
module
cmp.pipelines.anatomical
module
cmp.pipelines.anatomical.anatomical
module
cmp.pipelines.common
module
cmp.pipelines.diffusion
module
cmp.pipelines.diffusion.diffusion
module
cmp.pipelines.functional
module
cmp.pipelines.functional.eeg
module
cmp.pipelines.functional.fMRI
module
cmp.project
module
cmp.stages
module
cmp.stages.common
module
cmp.stages.connectome
module
cmp.stages.connectome.connectome
module
cmp.stages.connectome.fmri_connectome
module
cmp.stages.diffusion
module
cmp.stages.diffusion.diffusion
module
cmp.stages.diffusion.reconstruction
module
cmp.stages.diffusion.tracking
module
cmp.stages.functional
module
cmp.stages.functional.functionalMRI
module
cmp.stages.parcellation
module
cmp.stages.parcellation.parcellation
module
cmp.stages.preprocessing
module
cmp.stages.preprocessing.fmri_preprocessing
module
cmp.stages.preprocessing.preprocessing
module
cmp.stages.registration
module
cmp.stages.registration.registration
module
cmp.stages.segmentation
module
cmp.stages.segmentation.segmentation
module
cmp.viz
module
cmp.viz.reports
module
CMP_BIDSAppWindow (class in cmp.bidsappmanager.gui)
CMP_BIDSAppWindowHandler (class in cmp.bidsappmanager.project)
CMP_ConfigQualityWindowHandler (class in cmp.bidsappmanager.project)
CMP_ConfiguratorWindow (class in cmp.bidsappmanager.gui)
CMP_InspectorWindow (class in cmp.bidsappmanager.gui)
CMP_MainWindow (class in cmp.bidsappmanager.gui)
CMP_MainWindowHandler (class in cmp.bidsappmanager.project)
CMP_Project_Info (class in cmp.project)
CMP_Project_InfoUI (class in cmp.bidsappmanager.gui)
CMTK_cmat
cmtklib
module
,
[1]
cmtklib.bids
module
cmtklib.bids.utils
module
cmtklib.config
module
cmtklib.connectome
module
cmtklib.diffusion
module
cmtklib.functionalMRI
module
cmtklib.interfaces
module
cmtklib.interfaces.afni
module
cmtklib.interfaces.ants
module
cmtklib.interfaces.camino
module
cmtklib.interfaces.camino2trackvis
module
cmtklib.interfaces.diffusion_toolkit
module
cmtklib.interfaces.dipy
module
cmtklib.interfaces.freesurfer
module
cmtklib.interfaces.fsl
module
cmtklib.interfaces.misc
module
cmtklib.interfaces.mrtrix3
module
cmtklib.parcellation
module
cmtklib.util
module
CombineParcellations
compute_curvature (cmp.stages.connectome.connectome.ConnectomeConfig attribute)
compute_curvature_array() (in module cmtklib.connectome)
compute_length_array() (in module cmtklib.diffusion)
ComputeParcellationRoiVolumes
ConcatOutputsAsTuple
config (cmp.stages.common.Stage attribute)
config_view (cmp.bidsappmanager.stages.connectome.connectome.ConnectomeStageUI attribute)
(cmp.bidsappmanager.stages.connectome.fmri_connectome.ConnectomeStageUI attribute)
(cmp.bidsappmanager.stages.diffusion.diffusion.DiffusionStageUI attribute)
(cmp.bidsappmanager.stages.functional.functionalMRI.FunctionalMRIStageUI attribute)
(cmp.bidsappmanager.stages.parcellation.parcellation.ParcellationStageUI attribute)
(cmp.bidsappmanager.stages.preprocessing.fmri_preprocessing.PreprocessingStageUI attribute)
(cmp.bidsappmanager.stages.preprocessing.preprocessing.PreprocessingStageUI attribute)
(cmp.bidsappmanager.stages.registration.registration.RegistrationStageUI attribute)
(cmp.bidsappmanager.stages.segmentation.segmentation.SegmentationStageUI attribute)
configurator (cmp.bidsappmanager.gui.CMP_MainWindow attribute)
connectivity_metrics (cmp.bidsappmanager.stages.connectome.connectome.ConnectomeConfigUI attribute)
(cmp.stages.connectome.connectome.ConnectomeConfig attribute)
connectome (cmp.bidsappmanager.pipelines.diffusion.diffusion.DiffusionPipelineUI attribute)
(cmp.bidsappmanager.pipelines.functional.fMRI.fMRIPipelineUI attribute)
ConnectomeConfig (class in cmp.stages.connectome.connectome)
(class in cmp.stages.connectome.fmri_connectome)
ConnectomeConfigUI (class in cmp.bidsappmanager.stages.connectome.connectome)
(class in cmp.bidsappmanager.stages.connectome.fmri_connectome)
ConnectomeStage (class in cmp.stages.connectome.connectome)
(class in cmp.stages.connectome.fmri_connectome)
ConnectomeStageUI (class in cmp.bidsappmanager.stages.connectome.connectome)
(class in cmp.bidsappmanager.stages.connectome.fmri_connectome)
ConstrainedSphericalDeconvolution
contrast_type (cmp.stages.registration.registration.RegistrationConfig attribute)
convert_config_ini_2_json() (in module cmtklib.config)
copyBrainMaskToFreesurfer
copyFileToFreesurfer
create_annot_label() (in module cmtklib.parcellation)
create_configparser_from_pipeline() (in module cmtklib.config)
create_dipy_recon_flow() (in module cmp.stages.diffusion.reconstruction)
create_dipy_tracking_flow() (in module cmp.stages.diffusion.tracking)
create_endpoints_array() (in module cmtklib.connectome)
create_mrtrix_recon_flow() (in module cmp.stages.diffusion.reconstruction)
create_mrtrix_tracking_flow() (in module cmp.stages.diffusion.tracking)
create_parser() (in module cmp.cli.connectomemapper3)
create_pipeline_flow() (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline method)
(cmp.pipelines.diffusion.diffusion.DiffusionPipeline method)
(cmp.pipelines.functional.fMRI.fMRIPipeline method)
create_roi() (in module cmtklib.parcellation)
create_roi_v2() (in module cmtklib.parcellation)
create_stage_flow() (cmp.pipelines.common.Pipeline method)
create_subject_configuration_from_ref() (in module cmtklib.config)
create_T1_and_Brain() (in module cmtklib.parcellation)
create_view (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
create_wm_mask() (in module cmtklib.parcellation)
create_wm_mask_v2() (in module cmtklib.parcellation)
create_workflow() (cmp.stages.connectome.connectome.ConnectomeStage method)
,
[1]
(cmp.stages.connectome.fmri_connectome.ConnectomeStage method)
,
[1]
(cmp.stages.diffusion.diffusion.DiffusionStage method)
,
[1]
(cmp.stages.functional.functionalMRI.FunctionalMRIStage method)
,
[1]
(cmp.stages.parcellation.parcellation.ParcellationStage method)
,
[1]
(cmp.stages.preprocessing.fmri_preprocessing.PreprocessingStage method)
,
[1]
(cmp.stages.preprocessing.preprocessing.PreprocessingStage method)
,
[1]
(cmp.stages.registration.registration.RegistrationStage method)
,
[1]
(cmp.stages.segmentation.segmentation.SegmentationStage method)
,
[1]
CreateAcqpFile
CreateIndexFile
creation_mode (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
crop_and_move_datasets() (in module cmtklib.parcellation)
crop_and_move_WM_and_GM() (in module cmtklib.parcellation)
crop_at_gmwmi (cmp.stages.diffusion.tracking.MRtrix_tracking_config attribute)
CSD
csf (cmp.stages.functional.functionalMRI.FunctionalMRIConfig attribute)
custom_track_file (cmp.stages.diffusion.diffusion.DiffusionConfig attribute)
cutoff_value (cmp.stages.diffusion.tracking.MRtrix_tracking_config attribute)
D
data_provenance_tracking (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
datalad_dataset_path (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
datalad_is_available (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
datalad_update_environment (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
dataset_view (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
define_atlas_variables() (in module cmtklib.parcellation)
define_custom_mapping() (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline method)
(cmp.pipelines.diffusion.diffusion.DiffusionPipeline method)
(cmp.pipelines.functional.fMRI.fMRIPipeline method)
define_inspect_outputs() (cmp.stages.connectome.connectome.ConnectomeStage method)
(cmp.stages.connectome.fmri_connectome.ConnectomeStage method)
(cmp.stages.diffusion.diffusion.DiffusionStage method)
(cmp.stages.functional.functionalMRI.FunctionalMRIStage method)
(cmp.stages.parcellation.parcellation.ParcellationStage method)
(cmp.stages.preprocessing.fmri_preprocessing.PreprocessingStage method)
(cmp.stages.preprocessing.preprocessing.PreprocessingStage method)
(cmp.stages.registration.registration.RegistrationStage method)
(cmp.stages.segmentation.segmentation.SegmentationStage method)
denoising (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute)
denoising_algo (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute)
dep_check() (in module cmp.cli.cmpbidsappmanager)
(in module cmp.cli.connectomemapper3)
description (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute)
desired_number_of_tracks (cmp.stages.diffusion.tracking.MRtrix_tracking_config attribute)
Despike
despiking (cmp.stages.preprocessing.fmri_preprocessing.PreprocessingConfig attribute)
Detrending
DiffUnpack
diffusion (cmp.bidsappmanager.pipelines.diffusion.diffusion.DiffusionPipelineUI attribute)
diffusion_imaging_model (cmp.project.CMP_Project_Info attribute)
(cmp.stages.diffusion.diffusion.DiffusionConfig attribute)
(cmp.stages.registration.registration.RegistrationConfig attribute)
diffusion_imaging_model_editor (cmp.stages.diffusion.diffusion.DiffusionConfig attribute)
diffusion_imaging_model_select_view (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
diffusion_model (cmp.stages.diffusion.diffusion.DiffusionConfig attribute)
diffusion_model_editor (cmp.stages.diffusion.diffusion.DiffusionConfig attribute)
DiffusionConfig (class in cmp.stages.diffusion.diffusion)
DiffusionConfigUI (class in cmp.bidsappmanager.stages.diffusion.diffusion)
DiffusionPipeline (class in cmp.pipelines.diffusion.diffusion)
DiffusionPipelineUI (class in cmp.bidsappmanager.pipelines.diffusion.diffusion)
DiffusionStage (class in cmp.stages.diffusion.diffusion)
DiffusionStageUI (class in cmp.bidsappmanager.stages.diffusion.diffusion)
dilate_rois (cmp.stages.diffusion.diffusion.DiffusionConfig attribute)
dilation_kernel (cmp.stages.diffusion.diffusion.DiffusionConfig attribute)
dilation_radius (cmp.stages.diffusion.diffusion.DiffusionConfig attribute)
dipy_noise_model (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute)
Dipy_recon_config (class in cmp.stages.diffusion.reconstruction)
dipy_recon_config (cmp.stages.diffusion.diffusion.DiffusionConfig attribute)
Dipy_recon_configUI (class in cmp.bidsappmanager.stages.diffusion.reconstruction)
Dipy_tracking_config (class in cmp.stages.diffusion.tracking)
dipy_tracking_config (cmp.stages.diffusion.diffusion.DiffusionConfig attribute)
Dipy_tracking_configUI (class in cmp.bidsappmanager.stages.diffusion.tracking)
DirectionGetterTractography
discard_n_volumes (cmp.stages.preprocessing.fmri_preprocessing.PreprocessingConfig attribute)
Discard_tp
dmri_available (cmp.project.CMP_Project_Info attribute)
dmri_available_config (cmp.project.CMP_Project_Info attribute)
dmri_bids_acq (cmp.pipelines.diffusion.diffusion.Global_Configuration attribute)
(cmp.project.CMP_Project_Info attribute)
dmri_bids_acq_view (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
dmri_bids_acqs (cmp.project.CMP_Project_Info attribute)
dmri_config (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
dmri_config_error_msg (cmp.project.CMP_Project_Info attribute)
dmri_config_error_view (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
dmri_config_to_load (cmp.project.CMP_Project_Info attribute)
dmri_custom_last_stage (cmp.project.CMP_Project_Info attribute)
dmri_inputs_checked (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
(cmp.bidsappmanager.gui.CMP_InspectorWindow attribute)
(cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler attribute)
(cmp.bidsappmanager.project.CMP_MainWindowHandler attribute)
dmri_load_config_json() (in module cmtklib.config)
dmri_pipeline (cmp.bidsappmanager.gui.CMP_ConfiguratorWindow attribute)
(cmp.bidsappmanager.gui.CMP_InspectorWindow attribute)
(cmp.bidsappmanager.gui.CMP_MainWindow attribute)
(cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler attribute)
(cmp.bidsappmanager.project.CMP_MainWindowHandler attribute)
dmri_processed (cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler attribute)
(cmp.bidsappmanager.project.CMP_MainWindowHandler attribute)
dmri_run (cmp.project.CMP_Project_Info attribute)
dmri_runs (cmp.project.CMP_Project_Info attribute)
dmri_save_config (cmp.bidsappmanager.gui.CMP_ConfiguratorWindow attribute)
dmri_save_config() (in module cmtklib.config)
dmri_select_config_to_load (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
dmri_stage_names (cmp.project.CMP_Project_Info attribute)
dmri_warning_view (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
docker_process (cmp.bidsappmanager.project.CMP_BIDSAppWindowHandler attribute)
dof (cmp.stages.registration.registration.RegistrationConfig attribute)
DTIEstimateResponseSH
DTIRecon
DTLUTGen
DVARS_thr (cmp.stages.connectome.fmri_connectome.ConnectomeConfig attribute)
DWI2Tensor
DWIBiasCorrect
DWIDenoise
E
Eddy
eddy_correct_motion_correction (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute)
eddy_correction_algo (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute)
eddy_current_and_motion_correction (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute)
EddyOpenMP
Element (class in cmp.viz.reports)
enabled (cmp.stages.common.Stage attribute)
,
[1]
ENDC (cmtklib.util.BColors attribute)
Erode
,
[1]
erode_mask() (in module cmtklib.parcellation)
EstimateResponseForSH
extract() (in module cmtklib.parcellation)
extract_base_directory() (in module cmp.stages.segmentation.segmentation)
extract_freesurfer_subject_dir() (in module cmtklib.util)
ExtractFSLGrad
ExtractHeaderVoxel2WorldMatrix
ExtractImageVoxelSizes
ExtractMRTrixGrad
ExtractPVEsFrom5TT
F
fa_thresh (cmp.stages.diffusion.tracking.Dipy_tracking_config attribute)
FAIL (cmtklib.util.BColors attribute)
fast_use_priors (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute)
FD_thr (cmp.stages.connectome.fmri_connectome.ConnectomeConfig attribute)
fill_stages_outputs() (cmp.pipelines.common.Pipeline method)
filter_fibers() (in module cmtklib.diffusion)
FilterTractogram
flip_table_axis (cmp.bidsappmanager.stages.diffusion.reconstruction.Dipy_recon_configUI attribute)
(cmp.bidsappmanager.stages.diffusion.reconstruction.MRtrix_recon_configUI attribute)
(cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
(cmp.stages.diffusion.reconstruction.MRtrix_recon_config attribute)
FlipBvec
FlipTable
flirt_args (cmp.stages.registration.registration.RegistrationConfig attribute)
fmri_available (cmp.project.CMP_Project_Info attribute)
fmri_available_config (cmp.project.CMP_Project_Info attribute)
fmri_config (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
fmri_config_error_msg (cmp.project.CMP_Project_Info attribute)
fmri_config_error_view (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
fmri_config_to_load (cmp.project.CMP_Project_Info attribute)
fmri_custom_last_stage (cmp.project.CMP_Project_Info attribute)
fmri_inputs_checked (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
(cmp.bidsappmanager.gui.CMP_InspectorWindow attribute)
(cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler attribute)
(cmp.bidsappmanager.project.CMP_MainWindowHandler attribute)
fmri_load_config_json() (in module cmtklib.config)
fmri_pipeline (cmp.bidsappmanager.gui.CMP_ConfiguratorWindow attribute)
(cmp.bidsappmanager.gui.CMP_InspectorWindow attribute)
(cmp.bidsappmanager.gui.CMP_MainWindow attribute)
(cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler attribute)
(cmp.bidsappmanager.project.CMP_MainWindowHandler attribute)
fmri_processed (cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler attribute)
(cmp.bidsappmanager.project.CMP_MainWindowHandler attribute)
fmri_run (cmp.project.CMP_Project_Info attribute)
fmri_runs (cmp.project.CMP_Project_Info attribute)
fmri_save_config (cmp.bidsappmanager.gui.CMP_ConfiguratorWindow attribute)
fmri_save_config() (in module cmtklib.config)
fmri_select_config_to_load (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
fmri_stage_names (cmp.project.CMP_Project_Info attribute)
fmri_warning_view (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
fMRIPipeline (class in cmp.pipelines.functional.fMRI)
fMRIPipelineUI (class in cmp.bidsappmanager.pipelines.functional.fMRI)
freesurfer_args (cmp.stages.segmentation.segmentation.SegmentationConfig attribute)
freesurfer_subject_id (cmp.project.CMP_Project_Info attribute)
(cmp.stages.segmentation.segmentation.SegmentationConfig attribute)
freesurfer_subjects_dir (cmp.project.CMP_Project_Info attribute)
(cmp.stages.segmentation.segmentation.SegmentationConfig attribute)
fs_file (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
fs_subject_id (cmp.stages.registration.registration.RegistrationStage attribute)
fs_subjects_dir (cmp.stages.registration.registration.RegistrationStage attribute)
fsl_cost (cmp.stages.registration.registration.RegistrationConfig attribute)
FSLCreateHD
functionalMRI (cmp.bidsappmanager.pipelines.functional.fMRI.fMRIPipelineUI attribute)
FunctionalMRIConfig (class in cmp.stages.functional.functionalMRI)
FunctionalMRIConfigUI (class in cmp.bidsappmanager.stages.functional.functionalMRI)
FunctionalMRIStage (class in cmp.stages.functional.functionalMRI)
FunctionalMRIStageUI (class in cmp.bidsappmanager.stages.functional.functionalMRI)
G
gen_outputfilelist() (cmtklib.diffusion.Make_Seeds method)
Generate5tt
generate_name_title() (in module cmp.viz.reports)
generate_report() (cmp.viz.reports.Report method)
generate_reports() (in module cmp.viz.reports)
generate_single_parcellation() (in module cmtklib.parcellation)
generate_WM_and_GM_mask() (in module cmtklib.parcellation)
GenerateGMWMInterface
get() (in module cmp.parser)
get_anat_process_detail_json() (in module cmtklib.config)
get_dmri_process_detail_json() (in module cmtklib.config)
get_fmri_process_detail_json() (in module cmtklib.config)
get_freesurfer_parcellation() (in module cmp.stages.diffusion.tracking)
get_icon() (in module cmp.bidsappmanager.gui)
get_node_dictionary_outputs() (in module cmtklib.util)
get_parcellation() (in module cmtklib.parcellation)
get_pipeline_dictionary_outputs() (in module cmtklib.util)
get_process_detail_json() (in module cmtklib.config)
global_conf (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline attribute)
(cmp.pipelines.diffusion.diffusion.DiffusionPipeline attribute)
(cmp.pipelines.functional.fMRI.fMRIPipeline attribute)
Global_Configuration (class in cmp.pipelines.anatomical.anatomical)
(class in cmp.pipelines.diffusion.diffusion)
(class in cmp.pipelines.functional.fMRI)
global_nuisance (cmp.stages.functional.functionalMRI.FunctionalMRIConfig attribute)
group_analysis_sconn() (in module cmtklib.connectome)
H
HARDIMat
has_run() (cmp.stages.connectome.connectome.ConnectomeStage method)
(cmp.stages.connectome.fmri_connectome.ConnectomeStage method)
(cmp.stages.diffusion.diffusion.DiffusionStage method)
(cmp.stages.functional.functionalMRI.FunctionalMRIStage method)
(cmp.stages.parcellation.parcellation.ParcellationStage method)
(cmp.stages.preprocessing.fmri_preprocessing.PreprocessingStage method)
(cmp.stages.preprocessing.preprocessing.PreprocessingStage method)
(cmp.stages.registration.registration.RegistrationStage method)
(cmp.stages.segmentation.segmentation.SegmentationStage method)
HEADER (cmtklib.util.BColors attribute)
I
imaging_model (cmp.pipelines.functional.fMRI.Global_Configuration attribute)
(cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
(cmp.stages.diffusion.tracking.Dipy_tracking_config attribute)
include_thalamic_nuclei_parcellation (cmp.stages.parcellation.parcellation.ParcellationConfig attribute)
index() (cmp.viz.reports.Report method)
index_error_dir() (cmp.viz.reports.Report method)
info() (in module cmp.cli.cmpbidsappmanager)
(in module cmp.cli.connectomemapper3)
init (cmp.stages.registration.registration.RegistrationConfig attribute)
init_anat_project() (in module cmp.bidsappmanager.project)
(in module cmp.project)
init_dmri_project() (in module cmp.bidsappmanager.project)
(in module cmp.project)
init_fmri_project() (in module cmp.bidsappmanager.project)
(in module cmp.project)
input_folders (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline attribute)
(cmp.pipelines.diffusion.diffusion.DiffusionPipeline attribute)
(cmp.pipelines.functional.fMRI.fMRIPipeline attribute)
inspect_output_button (cmp.bidsappmanager.stages.connectome.connectome.ConnectomeStageUI attribute)
(cmp.bidsappmanager.stages.connectome.fmri_connectome.ConnectomeStageUI attribute)
(cmp.bidsappmanager.stages.diffusion.diffusion.DiffusionStageUI attribute)
(cmp.bidsappmanager.stages.functional.functionalMRI.FunctionalMRIStageUI attribute)
(cmp.bidsappmanager.stages.parcellation.parcellation.ParcellationStageUI attribute)
(cmp.bidsappmanager.stages.preprocessing.fmri_preprocessing.PreprocessingStageUI attribute)
(cmp.bidsappmanager.stages.preprocessing.preprocessing.PreprocessingStageUI attribute)
(cmp.bidsappmanager.stages.registration.registration.RegistrationStageUI attribute)
(cmp.bidsappmanager.stages.segmentation.segmentation.SegmentationStageUI attribute)
inspect_outputs (cmp.stages.common.Stage attribute)
,
[1]
inspect_outputs_enum (cmp.stages.common.Stage attribute)
inspect_outputs_view (cmp.bidsappmanager.stages.connectome.connectome.ConnectomeStageUI attribute)
(cmp.bidsappmanager.stages.connectome.fmri_connectome.ConnectomeStageUI attribute)
(cmp.bidsappmanager.stages.diffusion.diffusion.DiffusionStageUI attribute)
(cmp.bidsappmanager.stages.functional.functionalMRI.FunctionalMRIStageUI attribute)
(cmp.bidsappmanager.stages.parcellation.parcellation.ParcellationStageUI attribute)
(cmp.bidsappmanager.stages.preprocessing.fmri_preprocessing.PreprocessingStageUI attribute)
(cmp.bidsappmanager.stages.preprocessing.preprocessing.PreprocessingStageUI attribute)
(cmp.bidsappmanager.stages.registration.registration.RegistrationStageUI attribute)
(cmp.bidsappmanager.stages.segmentation.segmentation.SegmentationStageUI attribute)
install_datalad_dataset_via_ssh (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
interpolation (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute)
is_running() (cmp.stages.common.Stage method)
is_tool() (in module cmp.bidsappmanager.project)
ismember() (cmtklib.parcellation.CombineParcellations method)
isotropic_interpolation (cmp.stages.segmentation.segmentation.SegmentationConfig attribute)
isotropic_vox_size (cmp.stages.segmentation.segmentation.SegmentationConfig attribute)
L
laplacian_regularization (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
laplacian_weighting (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
launch_process() (cmp.pipelines.common.Pipeline method)
length() (in module cmtklib.util)
list_of_subjects_to_be_processed (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
lmax_order (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
(cmp.stages.diffusion.reconstruction.MRtrix_recon_config attribute)
load_anat_config_file() (cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler method)
load_dataset (cmp.bidsappmanager.gui.CMP_MainWindow attribute)
load_dataset() (cmp.bidsappmanager.project.CMP_MainWindowHandler method)
load_dmri_config_file() (cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler method)
load_fmri_config_file() (cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler method)
load_graphs() (in module cmtklib.util)
load_project() (cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler method)
local_model (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
(cmp.stages.diffusion.reconstruction.MRtrix_recon_config attribute)
local_model_editor (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
(cmp.stages.diffusion.reconstruction.MRtrix_recon_config attribute)
log_visualization (cmp.bidsappmanager.stages.connectome.connectome.ConnectomeStageUI attribute)
(cmp.bidsappmanager.stages.connectome.fmri_connectome.ConnectomeStageUI attribute)
(cmp.stages.connectome.connectome.ConnectomeConfig attribute)
(cmp.stages.connectome.fmri_connectome.ConnectomeConfig attribute)
M
magn() (in module cmtklib.util)
main() (in module cmp.cli.cmpbidsappmanager)
(in module cmp.cli.connectomemapper3)
(in module cmp.cli.showmatrix_gpickle)
make_isotropic (cmp.stages.segmentation.segmentation.SegmentationConfig attribute)
Make_Mrtrix_Seeds
Make_Seeds
manage_bidsapp_procs() (cmp.bidsappmanager.gui.CMP_BIDSAppWindow class method)
(cmp.bidsappmanager.project.CMP_BIDSAppWindowHandler class method)
manager_group (cmp.bidsappmanager.gui.CMP_MainWindow attribute)
MAPMRI
mapmri (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
MathsCommand
max_angle (cmp.stages.diffusion.tracking.Dipy_tracking_config attribute)
mean_curvature() (in module cmtklib.util)
modalities (cmp.pipelines.diffusion.diffusion.Global_Configuration attribute)
module
cmp
,
[1]
cmp.bidsappmanager
cmp.bidsappmanager.core
cmp.bidsappmanager.gui
cmp.bidsappmanager.images
cmp.bidsappmanager.pipelines
cmp.bidsappmanager.pipelines.anatomical
cmp.bidsappmanager.pipelines.anatomical.anatomical
cmp.bidsappmanager.pipelines.diffusion
cmp.bidsappmanager.pipelines.diffusion.diffusion
cmp.bidsappmanager.pipelines.functional
cmp.bidsappmanager.pipelines.functional.eeg
cmp.bidsappmanager.pipelines.functional.fMRI
cmp.bidsappmanager.project
cmp.bidsappmanager.stages
cmp.bidsappmanager.stages.connectome
cmp.bidsappmanager.stages.connectome.connectome
cmp.bidsappmanager.stages.connectome.fmri_connectome
cmp.bidsappmanager.stages.diffusion
cmp.bidsappmanager.stages.diffusion.diffusion
cmp.bidsappmanager.stages.diffusion.reconstruction
cmp.bidsappmanager.stages.diffusion.tracking
cmp.bidsappmanager.stages.functional
cmp.bidsappmanager.stages.functional.functionalMRI
cmp.bidsappmanager.stages.parcellation
cmp.bidsappmanager.stages.parcellation.parcellation
cmp.bidsappmanager.stages.preprocessing
cmp.bidsappmanager.stages.preprocessing.fmri_preprocessing
cmp.bidsappmanager.stages.preprocessing.preprocessing
cmp.bidsappmanager.stages.registration
cmp.bidsappmanager.stages.registration.registration
cmp.bidsappmanager.stages.segmentation
cmp.bidsappmanager.stages.segmentation.segmentation
cmp.cli
cmp.cli.cmpbidsappmanager
cmp.cli.connectomemapper3
cmp.cli.showmatrix_gpickle
cmp.parser
cmp.pipelines
cmp.pipelines.anatomical
cmp.pipelines.anatomical.anatomical
cmp.pipelines.common
cmp.pipelines.diffusion
cmp.pipelines.diffusion.diffusion
cmp.pipelines.functional
cmp.pipelines.functional.eeg
cmp.pipelines.functional.fMRI
cmp.project
cmp.stages
cmp.stages.common
cmp.stages.connectome
cmp.stages.connectome.connectome
cmp.stages.connectome.fmri_connectome
cmp.stages.diffusion
cmp.stages.diffusion.diffusion
cmp.stages.diffusion.reconstruction
cmp.stages.diffusion.tracking
cmp.stages.functional
cmp.stages.functional.functionalMRI
cmp.stages.parcellation
cmp.stages.parcellation.parcellation
cmp.stages.preprocessing
cmp.stages.preprocessing.fmri_preprocessing
cmp.stages.preprocessing.preprocessing
cmp.stages.registration
cmp.stages.registration.registration
cmp.stages.segmentation
cmp.stages.segmentation.segmentation
cmp.viz
cmp.viz.reports
cmtklib
,
[1]
cmtklib.bids
cmtklib.bids.utils
cmtklib.config
cmtklib.connectome
cmtklib.diffusion
cmtklib.functionalMRI
cmtklib.interfaces
cmtklib.interfaces.afni
cmtklib.interfaces.ants
cmtklib.interfaces.camino
cmtklib.interfaces.camino2trackvis
cmtklib.interfaces.diffusion_toolkit
cmtklib.interfaces.dipy
cmtklib.interfaces.freesurfer
cmtklib.interfaces.fsl
cmtklib.interfaces.misc
cmtklib.interfaces.mrtrix3
cmtklib.parcellation
cmtklib.util
motion (cmp.stages.functional.functionalMRI.FunctionalMRIConfig attribute)
motion_correction (cmp.stages.preprocessing.fmri_preprocessing.PreprocessingConfig attribute)
MRConvert
MRCrop
MRThreshold
MRTransform
MRTrix3Base
MRtrix_mul
MRtrix_recon_config (class in cmp.stages.diffusion.reconstruction)
mrtrix_recon_config (cmp.stages.diffusion.diffusion.DiffusionConfig attribute)
MRtrix_recon_configUI (class in cmp.bidsappmanager.stages.diffusion.reconstruction)
MRtrix_tracking_config (class in cmp.stages.diffusion.tracking)
mrtrix_tracking_config (cmp.stages.diffusion.diffusion.DiffusionConfig attribute)
MRtrix_tracking_configUI (class in cmp.bidsappmanager.stages.diffusion.tracking)
MultipleANTsApplyTransforms
MultiSelectAdapter (class in cmp.bidsappmanager.gui)
N
new_project() (cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler method)
no_search (cmp.stages.registration.registration.RegistrationConfig attribute)
now (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline attribute)
(cmp.pipelines.diffusion.diffusion.DiffusionPipeline attribute)
(cmp.pipelines.functional.fMRI.fMRIPipeline attribute)
Nuisance_regression
number_of_cores (cmp.pipelines.common.Pipeline attribute)
(cmp.project.CMP_Project_Info attribute)
number_of_parallel_procs_updated() (cmp.bidsappmanager.gui.CMP_BIDSAppWindow method)
number_of_participants_processed_in_parallel (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
number_of_seeds (cmp.stages.diffusion.tracking.Dipy_tracking_config attribute)
number_of_threads (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
(cmp.stages.segmentation.segmentation.SegmentationConfig attribute)
number_threads_max (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
O
OKBLUE (cmtklib.util.BColors attribute)
OKGREEN (cmtklib.util.BColors attribute)
open_view (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
order_by_run() (in module cmp.viz.reports)
ordered_stage_list (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline attribute)
(cmp.pipelines.diffusion.diffusion.DiffusionPipeline attribute)
(cmp.pipelines.functional.fMRI.fMRIPipeline attribute)
Orient
output_anat_available (cmp.bidsappmanager.gui.CMP_InspectorWindow attribute)
output_dir (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
(cmp.stages.common.Stage attribute)
output_directory (cmp.project.CMP_Project_Info attribute)
output_dmri_available (cmp.bidsappmanager.gui.CMP_InspectorWindow attribute)
output_fmri_available (cmp.bidsappmanager.gui.CMP_InspectorWindow attribute)
output_types (cmp.bidsappmanager.stages.connectome.connectome.ConnectomeConfigUI attribute)
(cmp.bidsappmanager.stages.connectome.fmri_connectome.ConnectomeConfigUI attribute)
(cmp.stages.connectome.connectome.ConnectomeConfig attribute)
(cmp.stages.connectome.fmri_connectome.ConnectomeConfig attribute)
P
Parcellate
ParcellateBrainstemStructures
ParcellateHippocampalSubfields
ParcellateThalamus
parcellation (cmp.bidsappmanager.pipelines.anatomical.anatomical.AnatomicalPipelineUI attribute)
parcellation_scheme (cmp.project.CMP_Project_Info attribute)
(cmp.stages.parcellation.parcellation.ParcellationConfig attribute)
parcellation_scheme_editor (cmp.stages.parcellation.parcellation.ParcellationConfig attribute)
ParcellationConfig (class in cmp.stages.parcellation.parcellation)
ParcellationConfigUI (class in cmp.bidsappmanager.stages.parcellation.parcellation)
ParcellationStage (class in cmp.stages.parcellation.parcellation)
ParcellationStageUI (class in cmp.bidsappmanager.stages.parcellation.parcellation)
partial_volume_estimation (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute)
PicoPDFs
Pipeline (class in cmp.pipelines.common)
pipeline (cmp.pipelines.common.ProcessThread attribute)
(cmp.stages.registration.registration.RegistrationConfig attribute)
pipeline_group (cmp.bidsappmanager.pipelines.anatomical.anatomical.AnatomicalPipelineUI attribute)
(cmp.bidsappmanager.pipelines.diffusion.diffusion.DiffusionPipelineUI attribute)
(cmp.bidsappmanager.pipelines.functional.fMRI.fMRIPipelineUI attribute)
pipeline_mode (cmp.stages.parcellation.parcellation.ParcellationConfig attribute)
pipeline_processing_summary_view (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
plot_connectivity_circle() (in module cmp.cli.showmatrix_gpickle)
positivity_constraint (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
preprocessing (cmp.bidsappmanager.pipelines.diffusion.diffusion.DiffusionPipelineUI attribute)
(cmp.bidsappmanager.pipelines.functional.fMRI.fMRIPipelineUI attribute)
PreprocessingConfig (class in cmp.stages.preprocessing.fmri_preprocessing)
(class in cmp.stages.preprocessing.preprocessing)
PreprocessingConfigUI (class in cmp.bidsappmanager.stages.preprocessing.fmri_preprocessing)
(class in cmp.bidsappmanager.stages.preprocessing.preprocessing)
PreprocessingStage (class in cmp.stages.preprocessing.fmri_preprocessing)
(class in cmp.stages.preprocessing.preprocessing)
PreprocessingStageUI (class in cmp.bidsappmanager.stages.preprocessing.fmri_preprocessing)
(class in cmp.bidsappmanager.stages.preprocessing.preprocessing)
print_blue() (in module cmtklib.util)
print_error() (in module cmtklib.util)
print_warning() (in module cmtklib.util)
process() (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline method)
(cmp.pipelines.diffusion.diffusion.DiffusionPipeline method)
(cmp.pipelines.functional.fMRI.fMRIPipeline method)
process_type (cmp.pipelines.anatomical.anatomical.Global_Configuration attribute)
(cmp.pipelines.diffusion.diffusion.Global_Configuration attribute)
(cmp.pipelines.functional.fMRI.Global_Configuration attribute)
processing_tool_editor (cmp.stages.diffusion.diffusion.DiffusionConfig attribute)
ProcessThread (class in cmp.pipelines.common)
ProgressThread (class in cmp.pipelines.common)
ProgressWindow (class in cmp.pipelines.common)
project_info (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
(cmp.bidsappmanager.gui.CMP_ConfiguratorWindow attribute)
(cmp.bidsappmanager.gui.CMP_InspectorWindow attribute)
(cmp.bidsappmanager.gui.CMP_MainWindow attribute)
project_loaded (cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler attribute)
(cmp.bidsappmanager.project.CMP_MainWindowHandler attribute)
pw (cmp.pipelines.common.ProgressThread attribute)
Q
quality_control (cmp.bidsappmanager.gui.CMP_MainWindow attribute)
R
radial_order (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
radial_order_values (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
recon_mode (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
(cmp.stages.diffusion.reconstruction.MRtrix_recon_config attribute)
recon_processing_tool (cmp.stages.diffusion.diffusion.DiffusionConfig attribute)
recon_processing_tool_editor (cmp.stages.diffusion.diffusion.DiffusionConfig attribute)
refresh_folder() (in module cmp.bidsappmanager.project)
(in module cmp.project)
registration (cmp.bidsappmanager.pipelines.diffusion.diffusion.DiffusionPipelineUI attribute)
(cmp.bidsappmanager.pipelines.functional.fMRI.fMRIPipelineUI attribute)
registration_mode (cmp.stages.registration.registration.RegistrationConfig attribute)
registration_mode_trait (cmp.stages.registration.registration.RegistrationConfig attribute)
RegistrationConfig (class in cmp.stages.registration.registration)
RegistrationConfigUI (class in cmp.bidsappmanager.stages.registration.registration)
RegistrationStage (class in cmp.stages.registration.registration)
RegistrationStageUI (class in cmp.bidsappmanager.stages.registration.registration)
repetition_time (cmp.stages.preprocessing.fmri_preprocessing.PreprocessingConfig attribute)
Report (class in cmp.viz.reports)
Reportlet (class in cmp.viz.reports)
resampling (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute)
return_button_style_sheet() (in module cmtklib.util)
ROI_idx (cmtklib.diffusion.Make_Mrtrix_Seeds attribute)
(cmtklib.diffusion.Make_Seeds attribute)
rsfmri_conmat
run() (cmp.bidsappmanager.gui.CMP_BIDSAppWindow class method)
(cmp.pipelines.common.ProcessThread method)
(cmp.pipelines.common.ProgressThread method)
(in module cmp.bidsappmanager.core)
run_anat_pipeline (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
run_dmri_pipeline (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
run_fmri_pipeline (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
run_individual() (in module cmp.project)
run_reports() (in module cmp.viz.reports)
S
save_all_config (cmp.bidsappmanager.gui.CMP_ConfiguratorWindow attribute)
save_anat_config_file() (cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler class method)
save_configparser_as_json() (in module cmtklib.config)
save_dmri_config_file() (cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler class method)
save_fibers() (in module cmtklib.connectome)
save_fmri_config_file() (cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler class method)
Scrubbing
SD (cmp.stages.diffusion.tracking.Dipy_tracking_config attribute)
(cmp.stages.diffusion.tracking.MRtrix_tracking_config attribute)
seed_density (cmp.stages.diffusion.tracking.Dipy_tracking_config attribute)
seed_from_gmwmi (cmp.stages.diffusion.tracking.Dipy_tracking_config attribute)
(cmp.stages.diffusion.tracking.MRtrix_tracking_config attribute)
seg_tool (cmp.stages.segmentation.segmentation.SegmentationConfig attribute)
segment_brainstem (cmp.stages.parcellation.parcellation.ParcellationConfig attribute)
segment_hippocampal_subfields (cmp.stages.parcellation.parcellation.ParcellationConfig attribute)
segmentation (cmp.bidsappmanager.pipelines.anatomical.anatomical.AnatomicalPipelineUI attribute)
SegmentationConfig (class in cmp.stages.segmentation.segmentation)
SegmentationConfigUI (class in cmp.bidsappmanager.stages.segmentation.segmentation)
SegmentationStage (class in cmp.stages.segmentation.segmentation)
SegmentationStageUI (class in cmp.bidsappmanager.stages.segmentation.segmentation)
select_subject() (cmp.bidsappmanager.gui.CMP_InspectorWindow method)
set_pipeline_attributes_from_config() (in module cmtklib.config)
sh_order (cmp.stages.diffusion.tracking.Dipy_tracking_config attribute)
SHORE
shore_constrain_e0 (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
shore_lambda_l (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
shore_lambda_n (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
shore_positive_constraint (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
shore_radial_order (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
shore_tau (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
shore_zeta (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
show_bidsapp_window() (cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler class method)
sift (cmp.stages.diffusion.tracking.MRtrix_tracking_config attribute)
SIFT2
single_fib_thr (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
(cmp.stages.diffusion.reconstruction.MRtrix_recon_config attribute)
slice_timing (cmp.stages.preprocessing.fmri_preprocessing.PreprocessingConfig attribute)
small_delta (cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
SplitDiffusion
ssh_remote (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
ssh_user (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
Stage (class in cmp.stages.common)
stage_names (cmp.pipelines.common.ProgressThread attribute)
stages (cmp.pipelines.common.ProgressThread attribute)
start_bids_app() (cmp.bidsappmanager.gui.CMP_BIDSAppWindow method)
(cmp.bidsappmanager.project.CMP_BIDSAppWindowHandler method)
start_bidsapp (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
start_bidsapp_participant_level_process() (cmp.bidsappmanager.gui.CMP_BIDSAppWindow method)
start_bidsapp_participant_level_process_with_datalad() (cmp.bidsappmanager.gui.CMP_BIDSAppWindow method)
start_bidsapp_process() (cmp.bidsappmanager.project.CMP_BIDSAppWindowHandler class method)
step_size (cmp.stages.diffusion.tracking.Dipy_tracking_config attribute)
stop_bids_app() (cmp.bidsappmanager.project.CMP_BIDSAppWindowHandler class method)
StreamlineTrack
strip_suffix() (in module cmp.stages.diffusion.diffusion)
subject (cmp.pipelines.anatomical.anatomical.Global_Configuration attribute)
(cmp.pipelines.common.Pipeline attribute)
(cmp.pipelines.diffusion.diffusion.Global_Configuration attribute)
(cmp.project.CMP_Project_Info attribute)
(cmp.stages.connectome.connectome.ConnectomeConfig attribute)
(cmp.stages.connectome.fmri_connectome.ConnectomeConfig attribute)
subject_session (cmp.pipelines.anatomical.anatomical.Global_Configuration attribute)
(cmp.pipelines.diffusion.diffusion.Global_Configuration attribute)
(cmp.project.CMP_Project_Info attribute)
subject_session_view (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
subject_sessions (cmp.project.CMP_Project_Info attribute)
subject_view (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
subjects (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
(cmp.pipelines.anatomical.anatomical.Global_Configuration attribute)
(cmp.pipelines.diffusion.diffusion.Global_Configuration attribute)
(cmp.project.CMP_Project_Info attribute)
SubReport (class in cmp.viz.reports)
summary_view_button (cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
T
t1_available (cmp.project.CMP_Project_Info attribute)
Tck2Trk
Tensor2Vector
TensorInformedEudXTractography
Tkregister2
total_readout (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute)
tracking_mode (cmp.stages.diffusion.tracking.Dipy_tracking_config attribute)
(cmp.stages.diffusion.tracking.MRtrix_tracking_config attribute)
tracking_processing_tool (cmp.stages.diffusion.diffusion.DiffusionConfig attribute)
(cmp.stages.diffusion.reconstruction.Dipy_recon_config attribute)
tracking_processing_tool_editor (cmp.stages.diffusion.diffusion.DiffusionConfig attribute)
traits_view (cmp.bidsappmanager.gui.CMP_BIDSAppWindow attribute)
(cmp.bidsappmanager.gui.CMP_ConfiguratorWindow attribute)
(cmp.bidsappmanager.gui.CMP_InspectorWindow attribute)
(cmp.bidsappmanager.gui.CMP_MainWindow attribute)
(cmp.bidsappmanager.gui.CMP_Project_InfoUI attribute)
(cmp.bidsappmanager.pipelines.anatomical.anatomical.AnatomicalPipelineUI attribute)
(cmp.bidsappmanager.pipelines.diffusion.diffusion.DiffusionPipelineUI attribute)
(cmp.bidsappmanager.pipelines.functional.fMRI.fMRIPipelineUI attribute)
(cmp.bidsappmanager.stages.connectome.connectome.ConnectomeConfigUI attribute)
(cmp.bidsappmanager.stages.connectome.fmri_connectome.ConnectomeConfigUI attribute)
(cmp.bidsappmanager.stages.diffusion.diffusion.DiffusionConfigUI attribute)
(cmp.bidsappmanager.stages.diffusion.reconstruction.Dipy_recon_configUI attribute)
(cmp.bidsappmanager.stages.diffusion.reconstruction.MRtrix_recon_configUI attribute)
(cmp.bidsappmanager.stages.diffusion.tracking.Dipy_tracking_configUI attribute)
(cmp.bidsappmanager.stages.diffusion.tracking.MRtrix_tracking_configUI attribute)
(cmp.bidsappmanager.stages.functional.functionalMRI.FunctionalMRIConfigUI attribute)
(cmp.bidsappmanager.stages.parcellation.parcellation.ParcellationConfigUI attribute)
(cmp.bidsappmanager.stages.preprocessing.fmri_preprocessing.PreprocessingConfigUI attribute)
(cmp.bidsappmanager.stages.preprocessing.preprocessing.PreprocessingConfigUI attribute)
(cmp.bidsappmanager.stages.registration.registration.RegistrationConfigUI attribute)
(cmp.bidsappmanager.stages.segmentation.segmentation.SegmentationConfigUI attribute)
U
UNDERLINE (cmtklib.util.BColors attribute)
unicode2str() (in module cmp.stages.registration.registration)
update_anat_last_processed() (in module cmp.bidsappmanager.project)
(in module cmp.project)
update_atlas_info() (cmp.stages.parcellation.parcellation.ParcellationConfig method)
update_checksettings() (cmp.bidsappmanager.gui.CMP_BIDSAppWindow method)
update_diffusion_imaging_model() (cmp.bidsappmanager.gui.CMP_ConfiguratorWindow method)
(cmp.bidsappmanager.gui.CMP_InspectorWindow method)
update_dipy_tracking_SD() (cmp.stages.diffusion.diffusion.DiffusionConfig method)
update_dipy_tracking_sh_order() (cmp.stages.diffusion.diffusion.DiffusionConfig method)
update_dmri_last_processed() (in module cmp.bidsappmanager.project)
(in module cmp.project)
update_fmri_last_processed() (in module cmp.bidsappmanager.project)
(in module cmp.project)
update_mrtrix_tracking_SD() (cmp.stages.diffusion.diffusion.DiffusionConfig method)
update_nuisance_requirements() (cmp.pipelines.functional.fMRI.fMRIPipeline method)
update_outputs_recon() (cmp.pipelines.diffusion.diffusion.DiffusionPipeline method)
update_outputs_tracking() (cmp.pipelines.diffusion.diffusion.DiffusionPipeline method)
update_parcellation() (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline method)
update_parcellation_scheme() (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline method)
update_registration() (cmp.pipelines.functional.fMRI.fMRIPipeline method)
update_run_anat_pipeline() (cmp.bidsappmanager.gui.CMP_BIDSAppWindow method)
update_run_dmri_pipeline() (cmp.bidsappmanager.gui.CMP_BIDSAppWindow method)
update_run_fmri_pipeline() (cmp.bidsappmanager.gui.CMP_BIDSAppWindow method)
update_scrubbing() (cmp.pipelines.functional.fMRI.fMRIPipeline method)
update_segmentation() (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline method)
update_subject_anat_pipeline() (cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler method)
update_subject_dmri_pipeline() (cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler method)
update_subject_fmri_pipeline() (cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler method)
update_vizualization_layout() (cmp.pipelines.diffusion.diffusion.DiffusionPipeline method)
update_vizualization_logscale() (cmp.pipelines.diffusion.diffusion.DiffusionPipeline method)
UpdateGMWMInterfaceSeeding
usage() (in module cmp.cli.cmpbidsappmanager)
use_act (cmp.stages.diffusion.tracking.Dipy_tracking_config attribute)
(cmp.stages.diffusion.tracking.MRtrix_tracking_config attribute)
use_existing_freesurfer_data (cmp.stages.segmentation.segmentation.SegmentationConfig attribute)
use_float_precision (cmp.stages.registration.registration.RegistrationConfig attribute)
use_fsl_brain_mask (cmp.stages.segmentation.segmentation.SegmentationConfig attribute)
uses_qform (cmp.stages.registration.registration.RegistrationConfig attribute)
V
view_mode (cmp.bidsappmanager.gui.CMP_MainWindow attribute)
(cmp.bidsappmanager.pipelines.anatomical.anatomical.AnatomicalPipelineUI attribute)
(cmp.bidsappmanager.pipelines.diffusion.diffusion.DiffusionPipelineUI attribute)
(cmp.bidsappmanager.pipelines.functional.fMRI.fMRIPipelineUI attribute)
Voxel2Image
W
WARNING (cmtklib.util.BColors attribute)
white_matter_mask (cmp.stages.segmentation.segmentation.SegmentationConfig attribute)
wm (cmp.stages.functional.functionalMRI.FunctionalMRIConfig attribute)
write_derivative_description() (in module cmtklib.bids.utils)
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v: v3.0.0-RC4
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