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This is a U.S. Government computer system, which may be accessed and used only for authorized Government business by authorized personnel. Unauthorized access or use of this computer system may subject violators to criminal, civil, and/or administrative action. All information on this computer system may be intercepted, recorded, read, copied, and disclosed by and to authorized personnel for official purposes, including criminal investigations. Such information includes sensitive data encrypted to comply with confidentiality and privacy requirements. Access or use of this computer system by any person, whether authorized or unauthorized, constitutes consent to these terms. There is no right of privacy in this system.

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Filter Cart

Viewable at the top right of NDA pages, the Filter Cart is a temporary holder for filters and data they select. Filters are added to the Workspace first, before being submitted to The Filter Cart. Data selected by filters in the Filter Cart can be added to a Data Package or an NDA Study from the Data Packaging Page, by clicking the 'Create Data Package / Add Data to Study' button.

The filter cart supports combining multiple filters together, and depending on filter type will use "AND" or "OR" when combining filters.

Multiple selections from the same filter type will result in those selections being applied with an ‘OR’ condition. For example, if you add an NDA Collection Filter with selections for both collections 2112 and 2563 to an empty Workspace, the subjects from NDA Collection 2112 ‘OR’ NDA Collection 2563 will be added to your Workspace even if a subject is in both NDA Collections. You can then add other NDA Collections to your Workspace which further extends the ‘OR’ condition.

If a different filter type is added to your Workspace, or a filter has already been submitted to the Filter Cart, the operation then performs a logical ‘AND’ operation. This means that given the subjects returned from the first filter, only those subjects that matched the first filter are returned by the second filter (i.e., subjects that satisfied both filters).

When combining other filters with the GUID filter, please note the GUID filter should be added last. Otherwise, preselected data may be lost. For example, a predefined filter from Featured Datasets may select a subset of data available for a subject. When combined with a GUID filter for the same subject, the filter cart will contain all data available from that subject, data structure, and dataset; this may be more data than was selected in the predefined filter for that subject. Again, you should add the GUID Filter as the last filter to your cart. This ensures 'AND' logic between filters and will limit results to the subjects, data structures, and datasets already included in your filter cart.

Note that only the subjects specific to your filter will be added to your Filter Cart and only on data shared with the research community. Other data for those same subjects may exist (i.e., within another NDA Collection, associated with a data structure that was not requested in the query, etc.). So, users should select ‘Find all Subjects Data’ to identify all data for those specific subjects.

Additional Tips:

  • You may query the data without an account, but to gain access you will need to create an NDA user account and apply for access. Most data access requires that you or your lab are sponsored by an NIH recognized institution with Federal Wide Assurance (FWA). Without access, you will not be able to obtain individual-level data.

Once you have selected data of interest you can:

  • Create a data package - This allows you to specify format for access/download
  • Assign to Study Cohort - Associate the data to an NDA Study allowing for a DOI to be generated and the data to be linked directly to a finding, publication, or data release.
  • Find All Subject Data - Depending on filter types being used, not all data associated with a subject will be selected. Data may be restricted by data structure, NDA Collection, or outcome variables (e.g., NDA Study). ‘Find All Data’ expands the filter criteria by replacing all filters in your Filter Cart with a single Query by GUID filter for all subjects selected by those filters.

Please Note:

  • When running a query, it may take a moment to populate the Filter Cart. Queries happen in the background so you can define other queries during this time.
  • When you add your first filter, all data associated with your query will be added to the Filter Cart (e.g., a Concept, an NDA Collection, a Data Structure/Element, etc.). As you add additional filters, they will also display in the Filter Cart. Only the name of filter will be shown in the Filter Cart, not the underlying structures.
  • Information about the contents of the Filter Cart can be seen by clicking "Edit”.
  • Once your results appear in the Filter Cart, you can create a data package or assign subjects to a study by selecting the 'Package/Assign to Study' option. You can also 'Edit' or 'Clear' filters.

Frequently Asked Questions

  • What is a Filter Cart?
    Viewable at the top right of NDA pages, the Filter Cart is a temporary holder of data identified by the user, through querying or browsing, as being of some potential interest. The Filter Cart is where you send the data from your Workspace after it has been filtered.
  • What do I do after filters are added to the Filter Cart?
    After filters are added to the Filter Cart, users have options to ‘Create a Package’ for download, ‘Associate to Study Cohort’, or ‘Find All Subject Data’. Selecting ‘Find All Subject Data’ identifies and pulls all data for the subjects into the Filter Cart. Choosing ‘Create a Package’ allows users to package and name their query information for download. Choosing ‘Associate to Study Cohort’ gives users the opportunity to choose the Study Cohort they wish to associate this data.
  • Are there limitations on the amount of data a user can download?

    NDA limits the rate at which individual users can transfer data out of Amazon Web Services (AWS) S3 Object storage to non-AWS internet addresses. All users have a download limit of 20 Terabytes. This limit applies to the volume of data an individual user can transfer within a 30-day window. Only downloads to non-AWS internet addresses will be counted against the limit.

  • How does Filter Cart Boolean logic work?

    The Filter Cart currently employs basic AND/OR Boolean logic. A single filter may contain multiple selections for that filter type, e.g., a single NDA Study filter might contain NDA Study 1 and NDA Study 2. A subject that is in EITHER 1 OR 2 will be returned. Adding multiple filters to the cart, regardless of type, will AND the result of each filter. If NDA Study 1 and NDA Study 2 are added as individual filters, data for a subject will only be selected if the subject is included in BOTH 1 AND 2.

    When combining other filters with the GUID filter, please note the GUID filter should be added last. Otherwise, preselected data may be lost. For example, a predefined filter from Featured Datasets may select a subset of data available for a subject. When combined with a GUID filter for the same subject, the filter cart will contain all data available from that subject, data structure, and dataset; this may be more data than was selected in the predefined filter for that subject. Again, you should add the GUID Filter as the last filter to your cart. This ensures 'AND' logic between filters and will limit results to the subjects, data structures, and datasets already included in your filter cart.

Glossary

  • Workspace
    The Workspace within the General Query Tool is a holding area where you can review your pending filters prior to adding them to Filter Cart. Therefore, the first step in accessing data is to select one or more items and move it into the Workspace.
  • Filter Cart
    Viewable at the top right of NDA pages, the Filter Cart is a temporary holder of data identified by the user through querying or browsing as being of some potential interest. The Filter Cart adds data using an AND condition. The opportunity to further refine data to determine what will be downloaded or sent to a miNDAR is available on the Data Packaging Page, the next step after the Filter Cart. Subsequent access to data is restricted by User Permission or Privilege; however Filter Cart use is not.
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Imaging_qa

1,565 Shared Subjects

QA for all imaging data
Neurosignal Recordings
Evaluated Data
05/30/2013
imaging_qa01
05/30/2013
View Change History
01
Definition
Submission Template
Query Element Name Data Type Size Required Description Value Range Notes Aliases
subjectkey GUID Required The NDAR Global Unique Identifier (GUID) for research subject NDAR*
src_subject_id String 20 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 :: 1260 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 20 Required Sex of subject at birth M;F; O; NR M = Male; F = Female; O=Other; NR = Not reported gender
Query experiment_id Integer Required ID for the Experiment/settings/run
file_source String 1,024 Required File name/location
Query external_min Float Required The minimum voxel intensity in the non-head region.
Query external_max Float Required The maximum voxel intensity in the non-head region.
Query external_robust_min Float Required The robust (2nd percentile) voxel intensity in the non-head region.
Query external_robust_max Float Required The robust (98th percentile) voxel intensity in the non-head region.
Query external_mean Float Required The mean voxel intensity in the non-head region.
Query external_std Float Required The standard deviation of voxel intensities in the non-head region.
Query external_voxels Integer Required The number of voxels in the non-head region.
Query external_volume Float Required The volume (in mm3) of the non-head region.
Query brain_min Float Required The minimum voxel intensity in the brain.
Query brain_max Float Required The maximum voxel intensity in the brain.
Query brain_robust_min Float Required The robust (2nd percentile) voxel intensity in the brain.
Query brain_robust_max Float Required The robust (98th percentile) voxel intensity in the brain.
Query brain_mean Float Required The mean voxel intensity in the brain.
Query brain_std Float Required The standard deviation of voxel intensities in the brain.
Query brain_voxels Integer Required The number of voxels in the brain.
Query brain_volume Float Required The volume (in mm3) of the brain.
Query csf_min Float Required The minimum voxel intensity in the CSF.
Query csf_max Float Required The maximum voxel intensity in the CSF.
Query csf_robust_min Float Required The robust (2nd percentile) voxel intensity in the CSF.
Query csf_robust_max Float Required The robust (98th percentile) voxel intensity in the CSF.
Query csf_mean Float Required The mean voxel intensity in the CSF.
Query csf_std Float Required The standard deviation of voxel intensities in the CSF.
Query csf_voxels Integer Required The number of voxels in the CSF.
Query csf_volume Float Required MRI Variables: CSF volume (mm3)
Query gm_min Float Required The minimum voxel intensity in the gray matter.
Query gm_max Float Required The maximum voxel intensity in the gray matter.
Query gm_robust_min Float Required The robust (2nd percentile) voxel intensity in the gray matter.
Query gm_robust_max Float Required The robust (98th percentile) voxel intensity in the gray matter.
Query gm_mean Float Required The mean voxel intensity in the gray matter.
Query gm_std Float Required The standard deviation of voxel intensities in the gray matter.
Query gm_voxels Integer Required The number of voxels in the gray matter.
Query gm_volume Float Required The volume (in mm3) of the gray matter.
Query wm_min Float Required The minimum voxel intensity in the white matter.
Query wm_max Float Required The maximum voxel intensity in the white matter.
Query wm_robust_min Float Required The robust (2nd percentile) voxel intensity in the white matter.
Query wm_robust_max Float Required The robust (98th percentile) voxel intensity in the white matter.
Query wm_mean Float Required The mean voxel intensity in the white matter.
Query wm_std Float Required The standard deviation of voxel intensities in the white matter.
Query wm_voxels Integer Required The number of voxels in the white matter.
Query wm_volume Float Required The volume (in mm3) of the white matter.
Query snr Float Required brain_mean/external_std brain_snr
Query input_pot_clipped_voxels Integer Required The number of potentially clipped voxels in the input volumes.
Query 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.
Query 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.
Query 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.
Query 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.
Query input_vols_mvd_1 Integer Required The number of input volumes with mean volume difference > 1%.
Query input_vols_mvd_2 Integer Required The number of input volumes with mean volume difference > 2%.
Query masked_mean_fwhm_x Float Required The mean FWHM in the X dimension of the masked volumes.
Query masked_mean_fwhm_y Float Required The mean FWHM in the Y dimension of the masked volumes.
Query masked_mean_fwhm_z Float Required The mean FWHM in the Z dimension of the masked volumes.
Query masked_detr_vols_run_diff_1 Integer Required The number of masked, detrended volumes with running difference > 1%.
Query masked_detr_vols_run_diff_2 Integer Required The number of masked, detrended volumes with running difference > 2%.
Query masked_detr_vols_1_outliers Integer Required The number of masked, detrended volumes
Query masked_detr_vols_2_outliers Integer Required The number of masked, detrended volumes
Query masked_detrended_mean Float Required The mean of the masked, detrended volume.
Query masked_detr_mean_snr1 Float Required The mean signal-to-noise ratio of the masked, detrended volumes.
Query masked_detr_mean_sfnr Float Required The mean signal-to-fluctuation-noise ratio of the masked, detrended volumes.
image_origin_check String 50 Required DTIPrep image origin check.
image_space_check String 50 Required DTIPrep image space check.
image_spaced_direction_check String 50 Required DTIPrep space direction check.
image_spacing_check String 50 Required DTIPrep image spacing check.
image_size_check String 50 Required DTIPrep image size check.
image_gradient_check String 50 Required DTIPrep image gradient check.
diffusion_meas_frame_check String 50 Required DTIPrep measurement frame check.
diffusion_slicewise_check String 50 Required DTIPrep slicewise check.
dwi_interlacewise_check String 50 Required DTIPrep interlacewise check.
dwi_gradientwise_check String 50 Required DTIPrep gradientwise check.
Query job_name String 50 Required Identity of the run for pipeline processes
Query origin_dataset_id Integer Required Origin dataset Id
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)
Query atlas String 255 Recommended Atlas
Query atlas_version String 255 Recommended Atlas version
derived_files File Recommended An archive of the files produced by the pipeline
Query img03_id Integer Recommended Corresponds to row_id in image03 data structure, mapping derivative to source record in image03
Query pipeline String 100 Recommended Pipeline name
Query pipeline_script String 255 Recommended File from pipeline used to derive output
Query pipeline_tools String 255 Recommended Specific tools used in a pipeline (i.e., FreeSurfer, FSL, ANTs)
Query pipeline_type String 255 Recommended Description of pipeline platform (i.e., LONI, NITRC-CE, NiPype)
Query pipeline_version String 255 Recommended Version assigned to pipeline
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 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 success String 8 Recommended Indicates QA test success or failure success; failure
comments_misc String 4,000 Recommended Miscellaneous comments on study, interview, methodology relevant to this form data
Query snr_b Integer Recommended brain_mean / brain_std
Query cnr Integer Recommended (wm_mean - gm_mean) / external_std wm - white matter; gm - gray matter; std - standard deviation
Query cnr_b Integer Recommended (wm_mean - gm_mean) / (.5 * (wm_std + gm_std)) wm - white matter; gm - gray matter; std - standard deviation
Query compl_file Integer Recommended Correct number of dicom files for the imaging sequence 0 :: 1 0=Incomplete; 1=Complete completed
Query abcd_compliant Integer Recommended Sequence parameters compliant with the ABCD imaging protocol 0 :: 1 0=Non ABCD Compliant; 1= ABCD Compliant
Query brain_tsnr_mean Float Recommended Mean value of temporal SNR within the brain
Query brain_tsnr_median Float Recommended Median value of temporal SNR within the brain
Query brain_tsnr_std Float Recommended Standard deviation of temporal SNR within the brain.
Query mean_motion Float Recommended Mean value of subject motion (framewise displacement) through time Reported in mm
Query subthresh_02 Float Recommended Absolute time with subject motion (framewise displacement) below 0.2 mm Reported in seconds
Query subthresh_03 Float Recommended Absolute time with subject motion (framewise displacement) below 0.3 mm Reported in seconds
Query subthresh_04 Float Recommended Absolute time with subject motion (framewise displacement) below 0.4 mm Reported in seconds
Query nbad_frame_slices Integer Recommended Number of bad slices for all frames
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)
  • For valid elements with shared data, on the far left is a Filter button you can use to view a summary of shared data for that element and apply a query filter to your Cart based on selected value ranges

At the top of this page you can also:

  • Use the search bar to filter the elements displayed. This will not filter on the Size of Required columns
  • Download a copy of this definition in CSV format
  • Download a blank CSV submission template prepopulated with the correct structure header rows ready to fill with subject records and upload

Please email the The NDA Help Desk with any questions.