Qu|Nex
  • Home
  • Get QuNex
  • About
  • Documentation
  • Forum
  • Home
  • Get QuNex
  • About
  • Documentation
  • Forum
  • Slider Image

QuNex documentation

  • Background
  • QuNex quick start

General overview

  • Overview
    • Batch files
    • Concatenation files
    • Event timing files
    • File formats overview
    • List files
    • Mapping specification files
    • Region of interest specification files
    • Session acquisition information files
    • Session pipeline information files
    • Organization of files and folders within a QuNex study
    • QuNex general usage overview
    • Logging and log files
    • QuNex quick start using a container
    • What is a Container?
    • Visual schematic of QuNex steps
  • What is a Container?
  • QuNex general usage overview
  • Visual schematic of QuNex steps
  • File formats overview
  • Organization of files and folders within a QuNex study
  • Logging and log files
  • HCP minimal preprocessing of HCP style DICOM data
  • HCP minimal preprocessing and denoising of HCP unprocessed data

User guides

  • UsageDocs
    • Functional connectivity analysis in QuNex
    • BOLD task-evoked and resting-state functional connectivity preprocessing
    • Running 1st and 2nd level BOLD task activation analyses
    • Visualizing data via CIFTI templates
    • Custom BOLD Regressors
    • Deidentifying DICOM files
    • Preparing study-level batch file and parameters for QuNex workflows
    • Group-level statistics and mapping results
    • HCP Diffusion pipeline
    • HCP fMRISurface pipeline
    • HCP fMRIVolume pipeline
    • HCP FreeSurfer pipeline
    • HCP ICAFix pipeline
    • HCP Longitudinal FreeSurfer
    • HCP Pipeline Mapping in QuNex
    • HCP MSMAll pipeline
    • HCP PostFreeSurfer pipeline
    • HCP PreFreeSurfer pipeline
    • General information on running the HCP pipeline
    • Overview of steps for running the HCP pipeline
    • HCP task fMRI analysis
    • Mapping processed data in and out of QuNex
    • Mapping HCP pipeline results to QuNex file hierarchy organization
    • BOLD movement scrubbing
    • Running quality control (QC) across modalities
    • Onboarding BIDS compliant data
    • Onboarding DICOM data and converting to NIfTI
    • Onboarding HCP formatted data
    • Onboarding new data into QuNex
    • Post-mortem macaque tractography
    • Preparing data for the HCP pipeline
    • On specification of processing parameters
    • Quality Assurance in QuNex
    • QuNex extensions
    • Identifying empirical ROI and extracting peak information
    • General overview
    • HCP ASL pipeline
    • HCP temporal ICA pipeline
    • Running commands over multiple sessions
    • Running the HCP pipeline
    • Running QuNex recipes
    • Parallel Execution and Scheduling of QuNex commands
    • Study level quality control summary
  • Running commands against a container using the qunex_container
  • Running QuNex recipes (chaining multiple commands in a sequence)
  • Running commands over multiple sessions
  • Parallel execution and Scheduling of QuNex commands
  • Using QuNex extensions
  • De-identifying DICOM files
  • Onboarding new data into QuNex
  • Preparing a study-level mapping file for QuNex workflows
  • Preparing study-level batch file and parameters for QuNex workflows
  • On specification of processing parameters
  • Preparing and running the HCP pipeline
  • Running quality control (QC) across modalities
  • Study level quality control summary
  • Running quality assurance (QA)
  • BOLD task-evoked and resting-state functional connectivity preprocessing
  • BOLD movement scrubbing
  • Running 1st and 2nd level BOLD task activation analyses
  • Running BOLD functional connectivity analyses
  • Group-level statistics and mapping of results
  • Identifying empirical ROI and extracting peak information
  • Visualizing data via CIFTI templates
  • Mapping processed data in and out of QuNex
  • Post-mortem macaque tractography

QuNex deployment in XNAT

  • QuNex-XNAT introduction and container setup
    • STEP 5: Launching the QuNex container for MRSession(s)
    • XNAT Management for advanced users & administrators
  • Launching the QuNex container in XNAT
  • XNAT management for advanced users and administrators

Specific command documentation

  • List of 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
Theme by the Executable Book Project
  • .rst

print_nifti_metadata

print_nifti_metadata#

qx_utilities.general.img.print_nifti_metadata(filename, info='list')#

print_nifti_metadata <image_filename> [info=list]

Print metadata extension blocks from a NIfTI file.

Parameters

--filename (str):

The path to the NIfTI file (.nii or .nii.gz)

--info (str, default 'list'):

Which metadata to print.

Possible values: - 'list': List metadata blocks without content (default) - 'all': Print all metadata blocks with full content - 'cifti': Print CIFTI metadata (ecode 32) - 'qunex' or 'qx': Print QuNex metadata (ecode 64) - Numeric code (e.g., 32, 64, 2, etc.): Print metadata with that code

Notes

NIfTI files can contain metadata extension blocks after the header. This function inspects and displays the content of these blocks.

METADATA CODES:

Common NIfTI extension codes: - 0: Unknown private format - 2: DICOM format - 4: AFNI group format - 6: Comment - 8: XCEDE format - 10: Jiffy XML format - 12: Unused - 14: Unused - 16: Unused - 18: MIND_IDENT format - 20: B_VALUE extension - 22: SPHERICAL_DIRECTION extension - 24: DT_COMPONENT extension - 26: SHC_DEGREEORDER extension - 28: VOXBO extension - 30: CARET extension - 32: CIFTI extension (XML format) - 34: VARIABLE_FRAME_TIMING extension - 36: MATLAB workspace extension - 38: QUANTIPHYSE extension - 40: MRS extension - 42: PYTHON pickle extension - 64: QuNex extension

Examples

::

# List metadata blocks (default) print_nifti_metadata('bold1.dtseries.nii')

# Print all metadata with full content print_nifti_metadata('bold1.dtseries.nii', info='all')

# Print only CIFTI metadata print_nifti_metadata('bold1.dtseries.nii', info='cifti')

# Print only QuNex metadata print_nifti_metadata('bold1.nii', info='qunex')

# Print metadata with specific numeric code print_nifti_metadata('bold1.nii', info=32) # CIFTI print_nifti_metadata('bold1.nii', info=6) # Comment

previous

preprocess_mice

next

printniftihdr

© Copyright 2026, Mind and Brain Lab (University of Ljubljana) and Cho Lab (Yale University).