List of commands
List of commands#
QuNex commands are used through the qunex call. The general use form is:
qunex <command_name> --parameter="<value>" --parameter="<value>" ...
For more information on how to use QuNex refer to QuNex commands and general usage overview.
Available commands:
- backup_files
- batch_tag2namekey
- bruker_to_dicom
- build_qx_container
- build_qx_extensions
- build_qx_registry
- change_dicom_files
- check_deprecated_commands
- check_fidl
- check_for_freesurfer_data
- check_study
- clean_dicom
- compare_nifti_images
- compare_snapshots
- compute_bold_fc
- compute_bold_stats
- copy_study
- create_batch
- create_bold_brain_masks
- create_bold_list
- create_conc
- create_conc_list
- create_list
- create_session_info
- create_stats_report
- create_study
- create_transmit_bias_voltages_file
- create_ws_palm_design
- dicom2nii
- dicom2niix
- dwi_bedpostx_gpu
- dwi_dtifit
- dwi_eddy_qc
- dwi_f99
- dwi_legacy_gpu
- dwi_noddi_gpu
- dwi_parcellate
- dwi_pre_tractography
- dwi_probtrackx_dense_gpu
- dwi_seed_tractography_dense
- dwi_xtract
- export_hcp
- extract_nuisance_signal
- extract_roi
- fc_compute_ab_corr
- fc_compute_ab_corr_kca
- fc_compute_gbc
- fc_compute_gbc3
- fc_compute_gbcd
- fc_compute_roifc
- fc_compute_seedmaps
- fc_compute_seedmaps_multiple
- fc_extract_roi_timeseries
- fc_extract_roi_timeseries_masked
- fc_extract_trial_timeseries_masked
- fc_preprocess
- fc_preprocess_conc
- fc_segment_mri
- fsl_feat
- fsl_melodic
- fz2zf
- gather_behavior
- general_compute_bold_list_stats
- general_compute_bold_stats
- general_compute_group_bold_stats
- general_convert_cifti
- general_create_roi
- general_extract_glm_volumes
- general_extract_roi_glm_values
- general_extract_roi_values
- general_find_peaks
- general_glm_predict
- general_image_conjunction
- general_image_overlap
- general_parcellated2dense
- general_plot_bold_timeseries
- general_plot_bold_timeseries_list
- general_qa_concfile
- general_remove_meta
- get_bold_data
- get_dicom_fields
- get_dicom_info
- hcp_apply_auto_reclean
- hcp_asl
- hcp_cortical_thickness
- hcp_dedrift_and_resample
- hcp_diffusion
- hcp_fmri_stats
- hcp_fmri_surface
- hcp_fmri_volume
- hcp_freesurfer
- hcp_icafix
- hcp_long_freesurfer
- hcp_long_msmall
- hcp_long_post_freesurfer
- hcp_long_transmit_bias
- hcp_make_average_dataset
- hcp_msmall
- hcp_nhp_freesurfer
- hcp_post_fix
- hcp_post_freesurfer
- hcp_pre_freesurfer
- hcp_prep_long
- hcp_reapply_fix
- hcp_run_qc
- hcp_task_fmri_analysis
- hcp_temporal_ica
- hcp_transmit_bias_group_average_corrected_maps
- hcp_transmit_bias_group_average_fit
- hcp_transmit_bias_individual
- hcp_transmit_bias_individual_adjustment
- hcp_transmit_bias_individual_align
- import_bids
- import_dicom
- import_dicom_old
- import_hcp
- import_nhp
- join_fidl
- join_fidl_folder
- join_maps
- list_dicom
- list_session_info
- list_sessions
- manage_study
- map2hcp
- map2pals
- map_bids2nii
- map_hcp_data
- map_hcpls2nii
- map_mice_data
- map_nii2bids
- mask_map
- meltmovfidl
- merge_session
- merge_sessions_list
- nifti24dfp
- parcellate_anat
- parcellate_bold
- prepare_slice_timing
- preprocess_bold
- preprocess_conc
- preprocess_mice
- print_nifti_metadata
- printniftihdr
- pull_sequence_names
- rapidtide
- record_snapshot
- remove_qunex_metadata
- reorder
- reslice
- restore_files
- rollback_snapshot
- run_basic_structural_segmentation
- run_freesurfer_full_segmentation
- run_freesurfer_subcortical_segmentation
- run_nil
- run_nil_folder
- run_palm
- run_qa
- run_qc
- run_qc_summary
- run_recipe
- run_shell_script
- schedule
- setup_hcp
- setup_mice
- slice_image
- sort_dicom
- split_dicom
- split_fidl
- stats_compute_behavioral_correlations
- stats_p2z
- stats_ttest_dependent
- stats_ttest_independent
- stats_ttest_zero