imaging_qa01 - Data Structure

Data Structure

Imaging_qa

Version 011563 Shared Subjects

Short Name: imaging_qa01

Data Type: Imaging

Categories: Evaluated Data

QA for all imaging data

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Definition

Submission Template

A Collection's submission must not be cumulative.

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Name	Type	Required	Description	Value Range	Notes
subjectkey	GUID	Required	The NDAR Global Unique Identifier (GUID) for research subject	NDAR*
src_subject_id	String	Required	Subject ID how it's defined in lab/project
interview_date	Date	Required	Date on which the interview/genetic test/sampling/imaging/biospecimen was completed. MM/DD/YYYY
interview_age	Integer	Required	Age in months at the time of the interview/test/sampling/imaging.	0::1440	Age is rounded to chronological month. If the research participant is 15-days-old at time of interview, the appropriate value would be 0 months. If the participant is 16-days-old, the value would be 1 month.
sex	String	Required	Sex of subject at birth	M;F; O; NR	M = Male; F = Female; O=Other; NR = Not reported
experiment_id	Integer	Required	ID for the Experiment/settings/run
file_source	String	Required	File name/location
external_min	Float	Required	The minimum voxel intensity in the non-head region.
external_max	Float	Required	The maximum voxel intensity in the non-head region.
external_robust_min	Float	Required	The robust (2nd percentile) voxel intensity in the non-head region.
external_robust_max	Float	Required	The robust (98th percentile) voxel intensity in the non-head region.
external_mean	Float	Required	The mean voxel intensity in the non-head region.
external_std	Float	Required	The standard deviation of voxel intensities in the non-head region.
external_voxels	Integer	Required	The number of voxels in the non-head region.
external_volume	Float	Required	The volume (in mm3) of the non-head region.
brain_min	Float	Required	The minimum voxel intensity in the brain.
brain_max	Float	Required	The maximum voxel intensity in the brain.
brain_robust_min	Float	Required	The robust (2nd percentile) voxel intensity in the brain.
brain_robust_max	Float	Required	The robust (98th percentile) voxel intensity in the brain.
brain_mean	Float	Required	The mean voxel intensity in the brain.
brain_std	Float	Required	The standard deviation of voxel intensities in the brain.
brain_voxels	Integer	Required	The number of voxels in the brain.
brain_volume	Float	Required	The volume (in mm3) of the brain.
csf_min	Float	Required	The minimum voxel intensity in the CSF.
csf_max	Float	Required	The maximum voxel intensity in the CSF.
csf_robust_min	Float	Required	The robust (2nd percentile) voxel intensity in the CSF.
csf_robust_max	Float	Required	The robust (98th percentile) voxel intensity in the CSF.
csf_mean	Float	Required	The mean voxel intensity in the CSF.
csf_std	Float	Required	The standard deviation of voxel intensities in the CSF.
csf_voxels	Integer	Required	The number of voxels in the CSF.
csf_volume	Float	Required	MRI Variables: CSF volume (mm3)
gm_min	Float	Required	The minimum voxel intensity in the gray matter.
gm_max	Float	Required	The maximum voxel intensity in the gray matter.
gm_robust_min	Float	Required	The robust (2nd percentile) voxel intensity in the gray matter.
gm_robust_max	Float	Required	The robust (98th percentile) voxel intensity in the gray matter.
gm_mean	Float	Required	The mean voxel intensity in the gray matter.
gm_std	Float	Required	The standard deviation of voxel intensities in the gray matter.
gm_voxels	Integer	Required	The number of voxels in the gray matter.
gm_volume	Float	Required	The volume (in mm3) of the gray matter.
wm_min	Float	Required	The minimum voxel intensity in the white matter.
wm_max	Float	Required	The maximum voxel intensity in the white matter.
wm_robust_min	Float	Required	The robust (2nd percentile) voxel intensity in the white matter.
wm_robust_max	Float	Required	The robust (98th percentile) voxel intensity in the white matter.
wm_mean	Float	Required	The mean voxel intensity in the white matter.
wm_std	Float	Required	The standard deviation of voxel intensities in the white matter.
wm_voxels	Integer	Required	The number of voxels in the white matter.
wm_volume	Float	Required	The volume (in mm3) of the white matter.
snr	Float	Required	brain_mean/external_std
input_pot_clipped_voxels	Integer	Required	The number of potentially clipped voxels in the input volumes.
input_vols_mi_abs_z_3_ind	Integer	Required	The number of input volumes with mean intensity greater than 3 standard deviations from the individual means.
input_vols_mi_abs_z_3_rgm	Integer	Required	The number of input volumes with mean intensity greater than 3 standard deviations from the grand mean.
input_vols_mi_abs_z_4_ind	Integer	Required	The number of input volumes with mean intensity greater than 4 standard deviations from the individual means.
input_vols_mi_abs_z_4_rgm	Integer	Required	The number of input volumes with mean intensity greater than 4 standard deviations from the grand mean.
input_vols_mvd_1	Integer	Required	The number of input volumes with mean volume difference > 1%.
input_vols_mvd_2	Integer	Required	The number of input volumes with mean volume difference > 2%.
masked_mean_fwhm_x	Float	Required	The mean FWHM in the X dimension of the masked volumes.
masked_mean_fwhm_y	Float	Required	The mean FWHM in the Y dimension of the masked volumes.
masked_mean_fwhm_z	Float	Required	The mean FWHM in the Z dimension of the masked volumes.
masked_detr_vols_run_diff_1	Integer	Required	"The number of masked, detrended volumes with running difference > 1%."
masked_detr_vols_run_diff_2	Integer	Required	"The number of masked, detrended volumes with running difference > 2%."
masked_detr_vols_1_outliers	Integer	Required	"The number of masked, detrended volumes"
masked_detr_vols_2_outliers	Integer	Required	"The number of masked, detrended volumes"
masked_detrended_mean	Float	Required	"The mean of the masked, detrended volume."
masked_detr_mean_snr1	Float	Required	"The mean signal-to-noise ratio of the masked, detrended volumes."
masked_detr_mean_sfnr	Float	Required	"The mean signal-to-fluctuation-noise ratio of the masked, detrended volumes."
image_origin_check	String	Required	DTIPrep image origin check.
image_space_check	String	Required	DTIPrep image space check.
image_spaced_direction_check	String	Required	DTIPrep space direction check.
image_spacing_check	String	Required	DTIPrep image spacing check.
image_size_check	String	Required	DTIPrep image size check.
image_gradient_check	String	Required	DTIPrep image gradient check.
diffusion_meas_frame_check	String	Required	DTIPrep measurement frame check.
diffusion_slicewise_check	String	Required	DTIPrep slicewise check.
dwi_interlacewise_check	String	Required	DTIPrep interlacewise check.
dwi_gradientwise_check	String	Required	DTIPrep gradientwise check.
job_name	String	Required	Identity of the run for pipeline processes
origin_dataset_id	Integer	Required	Origin dataset Id
scan_type	String	Required	Type of Scan	MR diffusion; fMRI; MR structural (MPRAGE); MR structural (T1); MR structural (PD); MR structural (FSPGR); MR structural (FISP); MR structural (T2); PET; ASL; microscopy; MR structural (PD, T2); MR structural (B0 map); MR structural (B1 map); single-shell DTI; multi-shell DTI; Field Map; X-Ray; static magnetic field B0; pCASL: ASL; MR: T2star; MR: FLAIR; Localizer scan; MR structural (FLASH); MR structural (MP2RAGE); MR structural (TSE); MR structural (T1, T2); 2D gradient echo; MR structural (MPnRAGE); Magnetic Resonance Spectroscopy(MRS); Neuromelanin MRI (NM-MRI); Functional Near Infrared Spectroscopy(fNIRS); MT; Magnetic Resonance Elastography (MRE); T1rho Spin-lock image; Image of Limb (IL); T2* Weighted Angiography (GE SWAN)
atlas	String	Recommended	Atlas
atlas_version	String	Recommended	Atlas version
derived_files	File	Recommended	An archive of the files produced by the pipeline
img03_id	Integer	Recommended	Corresponds to row_id in image03 data structure, mapping derivative to source record in image03
pipeline	String	Recommended	Pipeline name
pipeline_script	String	Recommended	File from pipeline used to derive output
pipeline_tools	String	Recommended	Specific tools used in a pipeline (i.e., FreeSurfer, FSL, ANTs)
pipeline_type	String	Recommended	Description of pipeline platform (i.e., LONI, NITRC-CE, NiPype)
pipeline_version	String	Recommended	Version assigned to pipeline
qc_fail_quest_reason	String	Recommended	Provide a reason that the image was determined to fail a quality control check or if the quality control check determined that the image was questionable
qc_outcome	String	Recommended	Provide information on the conclusion of the quality control methods regarding the quality of the image	pass;fail;questionable; undetermined; obsolete
success	String	Recommended	Indicates QA test success or failure	success; failure
comments_misc	String	Recommended	Miscellaneous comments on study, interview, methodology relevant to this form data
snr_b	Integer	Recommended	brain_mean / brain_std
cnr	Integer	Recommended	(wm_mean - gm_mean) / external_std		wm - white matter; gm - gray matter; std - standard deviation
cnr_b	Integer	Recommended	(wm_mean - gm_mean) / (.5 * (wm_std + gm_std))		wm - white matter; gm - gray matter; std - standard deviation
compl_file	Integer	Recommended	Correct number of dicom files for the imaging sequence	0 :: 1	0=Incomplete; 1=Complete
abcd_compliant	Integer	Recommended	Sequence parameters compliant with the ABCD imaging protocol	0 :: 1	0=Non ABCD Compliant; 1= ABCD Compliant
brain_tsnr_mean	Float	Recommended	Mean value of temporal SNR within the brain
brain_tsnr_median	Float	Recommended	Median value of temporal SNR within the brain
brain_tsnr_std	Float	Recommended	Standard deviation of temporal SNR within the brain.
mean_motion	Float	Recommended	Mean value of subject motion (framewise displacement) through time		Reported in mm
subthresh_02	Float	Recommended	Absolute time with subject motion (framewise displacement) below 0.2 mm		Reported in seconds
subthresh_03	Float	Recommended	Absolute time with subject motion (framewise displacement) below 0.3 mm		Reported in seconds
subthresh_04	Float	Recommended	Absolute time with subject motion (framewise displacement) below 0.4 mm		Reported in seconds
nbad_frame_slices	Integer	Recommended	Number of bad slices for all frames