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Get QuNex
About
Documentation
Forum
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QuNex documentation
Background
QuNex quick start
General overview
Overview
Installing from source and dependencies
Octave installation
PALM installation
Installation on macOS
What is a Container?
QuNex commands and general usage overview
File formats overview
Session acquisition information files
Session pipeline information files
Mapping specification files
Batch files
List files
Event timing files
Concatenation files
Region of interest specification files
Processing check files
QuNex data hierarchy specification
Logging and log files
Visual schematic of QuNex steps
BIDS support within QuNex
How to report issues with QuNex
User guides
Overview
General overview
QuNex 'turnkey' workflow and 'batch' engine
Running lists of QuNex commands
Running commands over multiple sessions
Parallel Execution and Scheduling of QuNex commands
De-identifying DICOM files
Preparing the QuNex study folder hierarchy
Onboarding new data into QuNex
Onboarding DICOM data and converting to NIfTI
Onboarding BIDS compliant data
Onboarding HCP formatted data
Preparing a study-level mapping file for QuNex workflows
Preparing study-level batch file and parameters for QuNex workflows
Preparing and running the HCP pipeline
General information on running the HCP pipeline
Preparing data for the HCP pipeline
Running the HCP pipeline
HCP PreFreeSurfer pipeline
HCP FreeSurfer pipeline
HCP PostFreeSurfer pipeline
HCP Longitudinal FreeSurfer
HCP fMRIVolume pipeline
HCP fMRISurface pipeline
HCP Diffusion pipeline
Diffusion weighted imaging (DWI) 'legacy' data preprocessing
HCP ICAFix pipeline
HCP MSMAll pipeline
HCP task fMRI analysis
HCP ASL pipeline
HCP temporal ICA pipeline
Mapping HCP pipeline results to QuNex file hierarchy organization
Running quality control (QC) across modalities
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
Diffusion weighted imaging (DWI) 'legacy' data preprocessing
Running DWI analyses
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
Launching the QuNex container in XNAT
XNAT management for advanced users and administrators
Specific command documentation
List of commands
bruker_to_dicom
change_dicom_files
check_fidl
compute_bold_stats
create_batch
create_bold_brain_masks
create_conc
create_list
create_session_info
create_stats_report
create_study
create_ws_palm_design
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
extract_nuisance_signal
extract_roi
fc_compute_ab_corr
fc_compute_ab_corr_kca
fc_compute_gbc3
fc_compute_gbcd
fc_compute_roifc
fc_compute_roifc_group
fc_compute_seedmaps
fc_compute_seedmaps_group
fc_compute_seedmaps_multiple
fc_extract_roi_timeseries_masked
fc_extract_trial_timeseries_masked
fc_preprocess
fc_preprocess_conc
fc_segment_mri
fsl_feat
fsl_melodic
general_compute_bold_list_stats
general_compute_bold_stats
general_compute_group_bold_stats
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
get_dicom_fields
hcp_apply_auto_reclean
hcp_asl
hcp_dedrift_and_resample
hcp_diffusion
hcp_fmri_surface
hcp_fmri_volume
hcp_freesurfer
hcp_icafix
hcp_longitudinal_freesurfer
hcp_make_average_dataset
hcp_msmall
hcp_post_fix
hcp_post_freesurfer
hcp_pre_freesurfer
hcp_reapply_fix
hcp_task_fmri_analysis
hcp_temporal_ica
import_bids
import_dicom
import_hcp
join_fidl
join_fidl_folder
map_hcp_data
map_mice_data
parcellate_anat
parcellate_bold
preprocess_bold
preprocess_conc
preprocess_mice
run_palm
run_qc
run_turnkey
setup_hcp
setup_mice
split_fidl
stats_compute_behavioral_correlations
stats_p2z
stats_ttest_dependent
stats_ttest_independent
stats_ttest_zero
Index
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
M
|
P
|
R
|
S
B
bruker_to_dicom() (in module qx_utilities.general.bruker)
C
change_dicom_files() (in module qx_utilities.general.dicomdeid)
check_fidl() (in module qx_utilities.general.fidl)
compute_bold_stats() (in module qx_utilities.processing.workflow)
create_batch() (in module qx_utilities.general.utilities)
create_bold_brain_masks() (in module qx_utilities.processing.workflow)
create_conc() (in module qx_utilities.general.utilities)
create_list() (in module qx_utilities.general.utilities)
create_session_info() (in module qx_utilities.general.utilities)
create_stats_report() (in module qx_utilities.processing.workflow)
create_study() (in module qx_utilities.general.utilities)
create_ws_palm_design() (in module qx_utilities.general.palm)
D
dwi_bedpostx_gpu() (in module qx_utilities.bash)
dwi_dtifit() (in module qx_utilities.bash)
dwi_eddy_qc() (in module qx_utilities.bash)
dwi_f99() (in module qx_utilities.processing.dwi)
dwi_legacy_gpu() (in module qx_utilities.bash)
dwi_noddi_gpu() (in module qx_utilities.processing.dwi)
dwi_parcellate() (in module qx_utilities.bash)
dwi_pre_tractography() (in module qx_utilities.bash)
dwi_probtrackx_dense_gpu() (in module qx_utilities.bash)
dwi_seed_tractography_dense() (in module qx_utilities.bash)
dwi_xtract() (in module qx_utilities.processing.dwi)
E
extract_nuisance_signal() (in module qx_utilities.processing.workflow)
extract_roi() (in module qx_utilities.bash)
F
fc_compute_ab_corr() (in module qx_mri.fc)
fc_compute_ab_corr_kca() (in module qx_mri.fc)
fc_compute_gbc3() (in module qx_mri.fc)
fc_compute_gbcd() (in module qx_mri.fc)
fc_compute_roifc() (in module qx_mri.fc)
fc_compute_roifc_group() (in module qx_mri.fc)
fc_compute_seedmaps() (in module qx_mri.fc)
fc_compute_seedmaps_group() (in module qx_mri.fc)
fc_compute_seedmaps_multiple() (in module qx_mri.fc)
fc_extract_roi_timeseries_masked() (in module qx_mri.fc)
fc_extract_trial_timeseries_masked() (in module qx_mri.fc)
fc_preprocess() (in module qx_mri.fc)
fc_preprocess_conc() (in module qx_mri.fc)
fc_segment_mri() (in module qx_mri.fc)
fsl_feat() (in module qx_utilities.processing.fsl)
fsl_melodic() (in module qx_utilities.processing.fsl)
G
general_compute_bold_list_stats() (in module qx_mri.general)
general_compute_bold_stats() (in module qx_mri.general)
general_compute_group_bold_stats() (in module qx_mri.general)
general_extract_glm_volumes() (in module qx_mri.general)
general_extract_roi_glm_values() (in module qx_mri.general)
general_extract_roi_values() (in module qx_mri.general)
general_find_peaks() (in module qx_mri.general)
general_glm_predict() (in module qx_mri.general)
general_image_conjunction() (in module qx_mri.general)
general_image_overlap() (in module qx_mri.general)
general_parcellated2dense() (in module qx_mri.general)
general_plot_bold_timeseries() (in module qx_mri.general)
general_plot_bold_timeseries_list() (in module qx_mri.general)
general_qa_concfile() (in module qx_mri.general)
get_dicom_fields() (in module qx_utilities.general.dicomdeid)
H
hcp_apply_auto_reclean() (in module qx_utilities.hcp.process_hcp)
hcp_asl() (in module qx_utilities.hcp.process_hcp)
hcp_dedrift_and_resample() (in module qx_utilities.hcp.process_hcp)
hcp_diffusion() (in module qx_utilities.hcp.process_hcp)
hcp_fmri_surface() (in module qx_utilities.hcp.process_hcp)
hcp_fmri_volume() (in module qx_utilities.hcp.process_hcp)
hcp_freesurfer() (in module qx_utilities.hcp.process_hcp)
hcp_icafix() (in module qx_utilities.hcp.process_hcp)
hcp_longitudinal_freesurfer() (in module qx_utilities.hcp.process_hcp)
hcp_make_average_dataset() (in module qx_utilities.hcp.process_hcp)
hcp_msmall() (in module qx_utilities.hcp.process_hcp)
hcp_post_fix() (in module qx_utilities.hcp.process_hcp)
hcp_post_freesurfer() (in module qx_utilities.hcp.process_hcp)
hcp_pre_freesurfer() (in module qx_utilities.hcp.process_hcp)
hcp_reapply_fix() (in module qx_utilities.hcp.process_hcp)
hcp_task_fmri_analysis() (in module qx_utilities.hcp.process_hcp)
hcp_temporal_ica() (in module qx_utilities.hcp.process_hcp)
I
import_bids() (in module qx_utilities.general.bids)
import_dicom() (in module qx_utilities.general.dicom)
import_hcp() (in module qx_utilities.hcp.import_hcp)
J
join_fidl() (in module qx_utilities.general.fidl)
join_fidl_folder() (in module qx_utilities.general.fidl)
M
map_hcp_data() (in module qx_utilities.hcp.process_hcp)
map_mice_data() (in module qx_mice.process_mice)
P
parcellate_anat() (in module qx_utilities.bash)
parcellate_bold() (in module qx_utilities.bash)
preprocess_bold() (in module qx_utilities.processing.workflow)
preprocess_conc() (in module qx_utilities.processing.workflow)
preprocess_mice() (in module qx_mice.process_mice)
R
run_palm() (in module qx_utilities.general.palm)
run_qc() (in module qx_utilities.bash)
run_turnkey() (in module qx_utilities.bash)
S
setup_hcp() (in module qx_utilities.hcp.setup_hcp)
setup_mice() (in module qx_mice.setup_mice)
split_fidl() (in module qx_utilities.general.fidl)
stats_compute_behavioral_correlations() (in module qx_mri.stats)
stats_p2z() (in module qx_mri.stats)
stats_ttest_dependent() (in module qx_mri.stats)
stats_ttest_independent() (in module qx_mri.stats)
stats_ttest_zero() (in module qx_mri.stats)