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NIMH Data Archive
NDA ABCD CCF OAI NIAAADA AMP SCZ HEAL

Image

53,325 Shared Subjects

N/A
Neurosignal Recordings
DTI, MRI, fMRI
10/20/2011
image03
11/15/2023
View Change History
03
Definition
Submission Template
Query Element Name Data Type Size Required Condition Description Value Range Notes Aliases
subjectkey GUID Required The NDAR Global Unique Identifier (GUID) for research subject NDAR* candidateguid, guid, pseudo_guid, subject_key
src_subject_id String 20 Required Subject ID how it's defined in lab/project child_id_full, cibsr_id_ndar, clinical_barcode, demo_study_id, ibisid, participant_id, participantid, pid, record_id, subject_id, subjid
interview_date Date Required Date on which the interview/genetic test/sampling/imaging/biospecimen was completed. MM/DD/YYYY ScanDate, assessment_dt, bl_visit_date, consentdate, consented_study, date_demographics, date_interview_ses, date_taken, fmri002, fmridt, interviewdate, intvdate, pfmridt, pp_date, profile_date, scan_date, scan_date_ndar, studydate, testing_date, visit_date
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. age_at_imgexam, age_m_consent, age_mri_ndar, candidate_age_in_months, intvage, scan_age, test_age, total_age_in_months
sex String 20 Required Sex of subject at birth
M;F; O; NR
M = Male; F = Female; O=Other; NR = Not reported gender, gender_mri_ndar, sex
comments_misc String 4,000 Recommended Miscellaneous comments on study, interview, methodology relevant to this form data Site, fspgod, scanner_ndar, site
image_file File Conditional isNull(manifest) Data file (image, behavioral, anatomical, etc) file_source
image_thumbnail_file Thumbnail Recommended Thumbnail
Query image_description String 512 Required Image description, i.e. DTI, fMRI, Fast SPGR, phantom, EEG, dynamic PET
Query experiment_id Integer Conditional scan_type == 'fMRI' ID for the Experiment/settings/run
Query scan_type String 50 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
Query scan_object String 50 Required The Object of the Scan (e.g. Live, Post-mortem, or Phantom Live; Post-mortem; Phantom
Query image_file_format String 50 Conditional isNull(manifest) Image file format AFNI; ANALYZE; AVI; BIORAD; BMP; BRIK; BRUKER; CHESHIRE; COR; DICOM; DM3; FITS; GE GENESIS; GE SIGNA4X; GIF; HEAD; ICO; ICS; INTERFILE; JPEG; LSM; MAGNETOM VISION; MEDIVISION; MGH; MICRO CAT; MINC; MIPAV XML; MRC; NIFTI; NRRD; OSM; PCX; PIC; PICT; PNG; QT; RAW; SPM; STK; TIFF; TGA; TMG; XBM; XPM; PARREC; MINC HDF; LIFF; BFLOAT; SIEMENS TEXT; ZVI; JP2; MATLAB; VISTA; ecat6; ecat7; PAR/REC; FIF; NIRS; DAT
data_file2 File 255 Recommended data file 2
Query data_file2_type String 100 Recommended data file 2 type/description
Query image_modality String 20 Required Image modality MRI; PET; CT; SPECT; ultrasound; FA; X-Ray; spectroscopy; microscopy; DEXA; fNIRS Computed Radiography; Computed Tomography; External Camera Photography; FA; General Microscopy; MRI; Magnetic Resonance; Magnetic Resonance Spectroscopy; Nuclear Medicine; Single Photon Emission Computed Tomography; Ultrasound
Query scanner_manufacturer_pd String 30 Conditional image_file_format != 'DICOM' && image_modality == 'MRI' Equipment Manufacturer camera_make, manufacturer, scanner_manufacturer
scanner_type_pd String 50 Conditional image_file_format != 'DICOM' && image_modality == 'MRI' Equipment Type/name ScannerID, camera_model, manufacturersmodelname, scanner_type
scanner_software_versions_pd String 100 Conditional image_file_format != 'DICOM' Aquisition/analysis Software Versions !=DICOM means not equal DICOM acquisiton_software, mmps_version, scanner_soft_versions_pd
Query magnetic_field_strength String 50 Conditional image_file_format != 'DICOM' && image_modality == 'MRI' Magnetic field strength magneticfieldstrength
Query mri_repetition_time_pd Float Conditional image_file_format != 'DICOM' && image_modality == 'MRI' Repetition Time (seconds) !=DICOM means not equal DICOM mri_repetition_time
Query mri_echo_time_pd String 100 Conditional image_file_format != 'DICOM' && image_modality == 'MRI' Echo Time (seconds) !=DICOM means not equal DICOM mri_echo_time
flip_angle String 30 Conditional image_file_format != 'DICOM' && image_modality == 'MRI' Flip angle !=DICOM means not equal DICOM
acquisition_matrix String 30 Conditional image_file_format != 'DICOM' && image_modality == 'MRI' Acquisition matrix !=DICOM means not equal DICOM
mri_field_of_view_pd String 50 Conditional image_file_format != 'DICOM' && image_modality == 'MRI' Field of View !=DICOM means not equal DICOM
Query patient_position String 50 Conditional image_file_format != 'DICOM' && image_modality == 'MRI' Patient position !=DICOM means not equal DICOM patientposition
Query photomet_interpret String 50 Conditional image_file_format != 'DICOM' && image_modality == 'MRI' Photometric interpretation !=DICOM means not equal DICOM
Query receive_coil String 50 Recommended Receive coil name
Query transmit_coil String 50 Recommended Transmit coil name
Query transformation_performed String 4 Required Performed transformation
Yes; No
Query transformation_type String 50 Conditional transformation_performed == 'Yes' Type of transformation
Query image_history String 1,024 Recommended Image history,f.e. transformations steps and other modifications.
Query image_num_dimensions Integer Conditional image_file_format != 'DICOM' Number of dimensions 1 :: 5 !=DICOM means not equal DICOM ndim
Query image_extent1 Integer Conditional image_file_format != 'DICOM' Extent [1] X dimension 1+ !=DICOM means not equal DICOM
Query image_extent2 Integer Conditional image_num_dimensions > 1 Extent [2] Y dimension 1+
Query image_extent3 Integer Conditional image_num_dimensions > 2 Extent [3] Z dimension 1+
Query image_extent4 Integer Conditional image_num_dimensions > 3 Extent [4]
Query extent4_type String 50 Conditional image_num_dimensions > 3 Description of extent [4]
Query image_extent5 Integer Conditional image_num_dimensions > 4 Extent [5] 1+
extent5_type String 50 Conditional image_num_dimensions > 4 Description of extent [5]
Query image_unit1 String 20 Conditional image_file_format != 'DICOM' Units [1] X dimension Inches; Centimeters; Angstroms; Nanometers; Micrometers; Millimeters; Meters; Kilometers; Miles; Nanoseconds; Microseconds; Milliseconds; Seconds; Minutes; Hours; Hertz; frame number !=DICOM means not equal DICOM
Query image_unit2 String 20 Conditional image_num_dimensions > 1 Units [2] Y dimension Inches; Centimeters; Angstroms; Nanometers; Micrometers; Millimeters; Meters; Kilometers; Miles; Nanoseconds; Microseconds; Milliseconds; Seconds; Minutes; Hours; Hertz; frame number
Query image_unit3 String 20 Conditional image_num_dimensions > 2 Units [3] Z dimension Inches; Centimeters; Angstroms; Nanometers; Micrometers; Millimeters; Meters; Kilometers; Miles; Nanoseconds; Microseconds; Milliseconds; Seconds; Minutes; Hours; Hertz; frame number
Query image_unit4 String 50 Conditional image_num_dimensions > 3 Units [4] Inches; Centimeters; Angstroms; Nanometers; Micrometers; Millimeters; Meters; Kilometers; Miles; Nanoseconds; Microseconds; Milliseconds; Seconds; Minutes; Hours; Hertz; Diffusion gradient; frame number; number of Volumes (across time)
Query image_unit5 String 20 Conditional image_num_dimensions > 4 Units [5] Inches; Centimeters; Angstroms; Nanometers; Micrometers; Millimeters; Meters; Kilometers; Miles; Nanoseconds; Microseconds; Milliseconds; Seconds; Minutes; Hours; Hertz; Diffusion gradient; frame number
Query image_resolution1 Float Conditional image_file_format != 'DICOM' Resolution [1] X dimension !=DICOM means not equal DICOM
Query image_resolution2 Float Conditional image_num_dimensions > 1 Resolution [2] Y dimension
Query image_resolution3 Float Conditional image_num_dimensions > 2 Resolution [3] Z dimension
Query image_resolution4 Float Conditional image_num_dimensions > 3 Resolution [4]
Query image_resolution5 Float Conditional image_num_dimensions > 4 Resolution [5]
Query image_slice_thickness Float Conditional image_file_format != 'DICOM' Slice thickness !=DICOM means not equal DICOM
Query image_orientation String 20 Conditional image_file_format != 'DICOM' Orientation Axial; Coronal; Sagittal !=DICOM means not equal DICOM
Query qc_outcome String 25 Recommended Provide information on the conclusion of the quality control methods regarding the quality of the image pass;fail;questionable; undetermined; obsolete
Query qc_description String 255 Recommended Provide information on the methods used to perform quality control checks on the image
Query qc_fail_quest_reason String 255 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
Query decay_correction String 10 Recommended Decay correction
frame_end_times String 50 Recommended Frame end times
frame_end_unit String 10 Recommended Frame end unit
frame_start_times String 50 Recommended Frame start times
frame_start_unit String 10 Recommended Frame start unit
Query pet_isotope String 50 Recommended PET isotope
Query pet_tracer String 100 Recommended PET tracer
Query time_diff_inject_to_image Integer Recommended Time difference injection to image
Query time_diff_units String 10 Recommended Time difference units
Query pulse_seq String 250 Recommended Information regarding the pulse sequence
Query slice_acquisition Integer Recommended fMRI slice acquisition 1::4 1=ascending; 2=descending; 3=interleaved-even first; 4=interleaved-odd first
Query software_preproc String 250 Recommended Software used for preprocessing/transformation of images (include version number)
study String 100 Recommended Study; The code for each individual study group
Query week Float Recommended Week in level/study 99=week 10-week 14
experiment_description String 4,000 Recommended Description of experiment/sequence/event name
Query visit String 60 Recommended Visit name assessment, visitid
slice_timing String 2,000 Conditional scan_type == 'fMRI' && image_file_format != 'DICOM' The time at which each slice was acquired during the acquisition. Slice timing is not slice order - it describes the time (sec) of each slice acquisition in relation to the beginning of volume acquisition. It is described using a list of times (in JSON format) referring to the acquisition time for each slice. The list goes through slices along the slice axis in the slice encoding dimension !=DICOM means not equal DICOM
Query bvek_bval_files String 5 Conditional scan_type == 'MR diffusion' || scan_type == 'multi-shell DTI' || scan_type == 'single-shell DTI' bvec and bval files provided as part of image_file or manifest Yes; No
bvecfile File Conditional bvek_bval_files=='No' Bvec file. The bvec files contain 3 rows with n space-delimited floating-point 5 numbers (corresponding to the n volumes in the relevant Nifti file). The first row contains the x elements, the second row contains the y elements and third row contains the z elements of a unit vector in the direction of the applied diffusion gradient, where the i-th elements in each row correspond together to the i-th volume with [0,0,0] for non-diffusion-weighted volumes bvec
bvalfile File Conditional bvek_bval_files=='No' Bval file. The bval file contains the b-values (in s/mm2) corresponding to the volumes in the relevant Nifti file), with 0 designating non-diffusion-weighted volumes, space-delimited bval
Query deviceserialnumber String 200 Recommended device serial number/ID
procdate Date Recommended data processed date
Query visnum Float Recommended Numeric Visit Number -1.5 = Pre-Screening; -1 = Screening; 0 = Baseline; ## = Visit ## (from 1 to 10); Whole numbers = standard monthly visits; #.001 - #.009 = Unscheduled; #.1 = End of Phase 1; #.2 = End of Phase 2; #.3 = End of Phase 3; #.4 = End of Open Choice Phase; #.5 = End of Study; #.6 = Genetic Analysis; 1000=all visits
manifest Manifest Conditional isNull(image_file)
emission_wavelingth Integer Conditional image_modality=='microscopy' && image_num_dimensions==2 emission wavelength in nanometers 100::1200
objective_magnification Float Conditional in_stack==1 magnification
objective_na Float Conditional in_stack==1 numerical aperture of objective lens 0.00::2.00
immersion Integer Conditional in_stack==1 immersion medium 0::3 0=none; 1=oil; 2=water; 3=glycerol
exposure_time Float Conditional in_stack==1 exposure time in seconds
camera_sn String 50 Conditional image_modality=='microscopy' serial number of camera
block_number Integer Recommended Block Number
level String 10 Recommended Treatment level
cut_thickness Float Conditional image_modality=='microscopy' cut thickness
stain String 50 Conditional image_modality=='microscopy' Stain used
stain_details String 200 Recommended Critical details of stainingi method, e.g. source and dilution of antibody for immunohistochemistry.
pipeline_stage Integer Conditional image_modality=='microscopy' Stage of image in processing pipeline. 1::3 1 = original; 2 = intermediate; 3 = final
deconvolved Integer Conditional image_modality=='microscopy' Was deconvolution used to obtain the image? 0::2 0 = no; 1 = yes; 2 = unknown
decon_software String 50 Conditional image_modality=='microscopy' deconvolution software
decon_method String 50 Conditional image_modality=='microscopy' Method of deconvolution.
psf_type String 1 Conditional image_modality=='microscopy' Type of point spread function used for deconvolution E; T E = empirical; T = theoretical
psf_file String 50 Conditional image_modality=='microscopy' Name of empirical point spread function file.
decon_snr Float Conditional image_modality=='microscopy' Signal to noise ratio used for deconvolution
decon_iterations Integer Conditional image_modality=='microscopy' Number of iterations used for deconvolution
micro_temmplate_name String 50 Conditional image_modality=='microscopy' Name of microscope template used for deconvolution
in_stack Integer Conditional image_modality=='microscopy' 2D image is part of 3D stack 0;1 0 = no; 1 = yes
decon_template_name String 50 Conditional image_modality=='microscopy' Name of deconvolution template used for deconvolution.
stack String 100 Conditional image_modality=='microscopy' Name of stack
slices Integer Conditional deconvolved == 1 Number of images in entire stack 2::2000
slice_number Integer Conditional deconvolved == 1 Sequence in stack 1::2000
slice_thickness Float Conditional deconvolved == 1 spacing between image planes, in microns
type_of_microscopy String 3 Conditional psf_type=='E' type of microscopy BF; WFF; CFF; 2P bright field, wide field fluorescensce, confocal fluorescensce, 2-photon
excitation_wavelength Integer Conditional deconvolved == 1 excitation wavelength in nanometers 100::1200
year_mta Integer Recommended Year in study visit_year
timepoint_label String 50 Recommended Timepoint/visit label
aqi Float Recommended AFNI?s quality index 0::1
fd_mean Float Recommended Mean frame wise displacement in mm 0::1
dvars_std Float Recommended Index the rate of change of BOLD signal across the entire brain at each frame of data 0::1.5 Higher value indicate higher variability
tsnr Float Recommended Temporal signal to noise ratio 0::100 0=Most noisy; 100=noise free signal
fetal_age Integer Recommended Age of the fetus (i.e., gestational age) in days 0::322
fetal_age_type Integer Recommended Type of gestational age used for fetal_age 1;2 1 = Postovulatory gestational age, defined as days since the last ovulation, expected term of 266 days; 2 = Postmenstrual gestational age, days since the last menstrual period, expected term of 280 days
accession_number String 20 Recommended Accession number of image analyzed barcode
ageyears Integer Recommended Age in years
iti_onset Integer Recommended Time since beginning of experiment (ms) to onset of inter-trial interval at the end of the current trial
stim1 String 200 Recommended Description of stimulus 1 (e.g. cross, triangle, square, circle)
stim2 String 200 Recommended Description of stimulus 2 (e.g. cross, triangle, square, circle)
stim1_side Integer Recommended On which side was stim1 presented 1;2 1 = Left; 2 = Right
stim1_magnitude Integer Recommended Magnitude of stim1 1 :: 99
stim2_magnitude Integer Recommended Magnitude of stim2 1 :: 99
choice_side Integer Recommended On which side was the selected option located? 1;2 1 = Left, chose left shape; 2 = Right, chose right shape
computer_choice Integer Recommended Response randomly selected by the computer due to timeout 0;1 1 = Computer made the choice; 0 = Participant made the choice
stim1_outcome Integer Recommended Information whether stim1 is associated with a non-zero outcome on the current trial 0;1 1 = Stim1 results in the non-zero outcome; 0 = Stim2 results in the non-zero outcome. Non-zero outcome = reward or shock receipt
session_fmri String 50 Recommended First or second fMRI session (e.g. fmri1, fmri2) session
choice_fmri Integer Recommended Selected stimulus option 0;1 1 = stim1; 0 = stim2 choice
outcome_fmri Integer Recommended Final outcome of a trial 0;1 1 = Non-zero outcome (reward/shock received); 0 = Zero outcome (reward/shock not received) outcome
rt_fmri Integer Recommended Response time (ms) 0::9999 9999 = timeout, i.e. > 4000ms rt
task__version Integer Recommended Task version 1;2 1 = Shock; 2 = Reward-gain task_version
block_sv Integer Recommended Did block involve volatile or stable condition? 1;2 1 = Stable; 2 = Volatile; counter-balanced across participants block
trial_num Integer Recommended Trial number within a block 1::180
options_onset Integer Recommended Time since beginning of experiment (ms) to presentation of options in the current trial
cue_onset Integer Recommended Time since beginning of experiment (ms) to onset of response period in the current trial
interval_onset Integer Recommended Time since beginning of experiment (ms) to response in the current trial
monitor_onset Integer Recommended Time since beginning of experiment (ms) to outcome presentation in the current trial
session_det String 250 Recommended session details
gbc Float Recommended Global Brain Connectivity
vtca Float Recommended Glial oxidative metabolism
vtcan Float Recommended Glutamate neurotransmission strength
eventname String 60 Recommended The event name for which the data was collected
taskname String 50 Recommended Name of the task. No two tasks should have the same name. Task label (task-) included in the file name is derived from this field by removing all non alphanumeric ([a-zA-Z0-9]) characters. For example task name faces n-back will corresponds to task label facesnback. A RECOMMENDED convention is to name resting state task using labels beginning with rest.
abbrev_taskname String 30 Recommended abbrev_taskname
vendor String 100 Recommended Vendor
Data Structure

This page displays the data structure defined for the measure identified in the title and structure short name. The table below displays a list of data elements in this structure (also called variables) and the following information:

  • Element Name: This is the standard element name
  • Data Type: Which type of data this element is, e.g. String, Float, File location.
  • Size: If applicable, the character limit of this element
  • Required: This column displays whether the element is Required for valid submissions, Recommended for valid submissions, Conditional on other elements, or Optional
  • Description: A basic description
  • Value Range: Which values can appear validly in this element (case sensitive for strings)
  • Notes: Expanded description or notes on coding of values
  • Aliases: A list of currently supported Aliases (alternate element names)
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