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   *Some sections were further divided. See photos for tissue location.

Contents

  1. Target Outcome
  2. Data File/Folder Naming Convention
    1. Specimen Configuration File
    2. Binary Data File
    3. File Naming Convention - Imaging
    4. File Naming Convention - Image Registration
    5. File Naming Convention - Mechanical Testing
    6. File Naming Convention - Video Recording of Indentation
    7. Folder Structure

Target Outcome

  • To establish a naming convention for specimens, files, and folders for in vitro experimentation

Data File/Folder Naming Convention

note: similar protocol for in vivo with the following exceptions

  • Subjects are referred to as donors
    • Each right leg and arm will come from one donor
  • Lifestyle i.e. Extremely Active, is not known for cadaver specimen

Specimen Configuration File

  • Specimen data is stored in a subject configuration file (.xml format)
  • Specimens are identified by a number
  • Specimen information includes:

    • Donor ID (Convention is CMULTISXXX-Y where XXX is auto incremented unique for each Donor. Y is a number starting at 1. This tag is auto incremented if the operator chooses to retest the subject 2, -3, etc.).

    • Test Date
    • Test Type (New or retest)
    • Demographics
      1. Age
      2. Gender
      3. Ethnicity
      4. Race
      5. Height
      6. Body Mass
    • Collected Data Structure - An array of structures of the following data elements
      1. Ultrasound Location
      2. Data collected (boolean)
      3. Location File Abbreviation
      4. Data File Array - Each ultrasound location may be measured more than once. Data is never deleted. Displayed data will always be the last element in the array.
        1. Path on disk
        2. Data accepted (Boolean)
        3. Time Stamp
        4. Experiment Run Number - This is the same number that was transmitted to the ultrasound machine via the signal outlined above.
  • Data File Example

Example_Specimen_Configuration.xml

Binary Data File

  • Force and orientation data will be stored in a binary TDMS data file. TDMS is a proprietary National Instruments file format, but there are many readers (open source and otherwise) that can be used to read in the data from these files.
  • File contents:
    • Group/Channel
      • Sensor.500 N Range - FT17991/Fx
      • Sensor.500 N Range - FT17991/Fy
      • Sensor.500 N Range - FT17991/Fz
      • Sensor.500 N Range - FT17991/Mx
      • Sensor.500 N Range - FT17991/My
      • Sensor.500 N Range - FT17991/Mz
      • Run Number Pulse Train/Value
      • Sensor.Orientation/wQuaternion
      • Sensor.Orientation/xQuaternion
      • Sensor.Orientation/yQuaternion
      • Sensor.Orientation/zQuaternion
      • State.Transformed Load/Fx
      • State.Transformed Load/Fy
      • State.Transformed Load/Fz
      • State.Transformed Load/Mx
      • State.Transformed Load/My
      • State.Transformed Load/Mz
  • File Naming Convention - Ultrasound
    1. "Experiment Run Number"_"Donor ID"_"Limb Segment"_"Location"_"Test Type"-"Trial Number Index".tdms Where:
      • Experiment Run Number: 3 digit number that gets auto-incremented for each tdms file (order in which data is collected for each specimen)
      • Specimen ID
      • Limb Segment:
        • (UA) Upper Arm,
        • (UL) Upper Leg,
        • (LA) Lower Arm,
        • (LL) Lower Leg
      • Location: Two letters
        • First Letter
          • (A)nterior
          • (P)osterior
          • (M)edial
          • (L)ateral
        • Second Letter
          • (P)roximal
          • (D)istal
          • (C)entral
      • Test Type:
        • I = Indentation
        • A = Anatomy (no indentation)
      • Trial Number Index: auto-incremented for each trial. i.e. if the location is tested more than once the subsequent data files will be -2, -3, etc.
    2. Example Data File Name: 034_CMULTIS033-2_UA_AP_I-4.tdms

File Naming Convention - Imaging

  1. Combined DICOM converted to NIFTI image format (CT)
    • "Donor ID"_Segment_CT.nii (example: CMULTIS001-1_WL_CT.nii)
  2. Combined DICOM converted to NIFTI image format (MRI)
    • MRI_"DONOR ID"_"Segment"_"Acquisition Properties".nii Where:
      • Segment
        • UL = Upper Leg
        • LL = Lower Leg
        • UA = Upper Arm
        • LA = Lower Arm
        • WL = Whole Leg
        • WA = Whole Arm
      • Acquisition Properties

        • T1 = T1-weighted without fat suppression

        • FS = T1-weighted with fat suppression

    • Example File Name: CMULTIS002-3_UA_MRI_T1.nii

File Naming Convention - Image Registration

  1. Registration Marker STLs
    • Follows imaging convention with the the appropriate fiducial marker label added (F = Femur, T = Tibia, H = Humerus, R = Radius).
      • CT Example: CMULTIS002-1_F2_CT, which corresponds to the second fiducial marker of the femur bone.
      • MRI Example: CMULTIS002-3_R1_MR, which corresponds to the first fiducial marker of the radius bone of the T1-weighted image set.

File Naming Convention - Mechanical Testing

  1. "Experiment Run Number"_"Donor ID"_"Limb Segment"_"Location"_"Tissue"_"Shape"_"Orientation"_"Test Type"-"Trial Number Index".txt
  2. Similar to naming convention above with the following exceptions
  • Where:
    • Donor ID
    • Limb Segment:
      • (UA) Upper Arm,
      • (UL) Upper Leg,
      • (LA) Lower Arm,
      • (LL) Lower Leg
    • Tissue
      • (S)kin
      • (F)at
      • (M)uscle
      • (SF) Skin-Fat interface
      • (SM) Skin-Muscle interface
      • (FM) Fat-Muscle interface
      • (MM) Muscle-Muscle interface
    Location: Two letters
    • First Letter
      • A)nterior
      • (P)osterior
      • (M)edial
      • (L)ateral
      Second Letter
      • (P)roximal
      • (D)istal
      • (C)entral
    • Orientation
      • (CI) Across Interface
      • (LI)Along Interface
      • (0) degrees
      • (45) degrees
      • (90) degrees
    • Test Type
      • (T)ensile
      • (UC) Unconfined Compression
      • (CC) Confined Compression
    • Some sections were further divided. See photos for tissue location.

File Naming Convention - Video Recording of Indentation

  • Same as TDMS naming convention with following exceptions
    • ".mp4" extension
    • Camera Number (1,2,3,4)
    • "Donor ID"_"Limb Segment"_"Camera Number".mp4

Folder Structure

  • Software will be located in the following folder

    1. C:\Program Files\National Instruments\LabVIEW 2013\vi.lib\BioRobotics\Linus

      1. Configuration (contains master Subject Configuration File, Sensor configuration files, Ultrasound Locations)
  • Data will be sorted into the following folder convention
    1. Drive (e.g. C:)
      1. Test Cell (MULTIS Data)
        1. Subject (Subject ID number)
          1. Configuration (contains the single subject configuration file)
          2. Data (contains all the binary data files)

Specifications/Labeling (last edited 2020-02-12 15:19:59 by klonowe)