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ptokarcz edited this page Apr 19, 2019 · 11 revisions

Data organisation

(1) to (5) infer folder levels

(1) All 2D and 4D flow data are located in the following directory: S:\4-D Flow MRI

(2) To obtain 2D and 4D flow data refer to “2D FLOW MRI DATA” and “4D FLOW MRI DATA” folders.

(3) “2D FLOW MRI DATA” were acquired in 2 different planes. Refer to “Aorta Sagittal Plane” and “Aorta Transverse Plane” folders. “4D FLOW MRI DATA” contains 3 sub-folders; “COHORT STUDIES”, “VOLUNTEER STUDIES” and “OTHER STUDIES”. Please only refer to “COHORT STUDIES” and “VOLUNTEER STUDIES”.

(4) For “2D FLOW MRI DATA” when locating input and output images select the Venc required. Both “Aorta Sagittal Plane” and “Aorta Transverse Plane” contain 9 Vencs, from 40cm/s to 200cm/s. Note: 40 to 180 (treated as “low”) are merged to Venc 200 (treated as “high”). Input data contain single-sliced 2D phase contrast (PC) data at 30 time- frames.

    For “4D FLOW MRI DATA” when locating input and output images select the study group required “COHORT STUDIES” or 
    “VOLUNTEER STUDIES”. Following this select subject i.e. “3T7164” in “COHORT STUDIES” or “3T7200” in “VOLUNTEER 
    STUDIES”. For each subject there is a high-Venc and low-Venc folder. High-Venc and Low-Venc folders contain three 
    PC folders and one magnitude sum folder.

(5) To locate dual-Venc or merged data in the “2D FLOW MRI DATA” folder – select the Venc required, then select folders titled “MERGED”. To locate dual-Venc or merged data in the “4D FLOW MRI DATA” folder – select the subject, then select “RIGID REGISTRATION”, then select the dual-Venc encoding direction. All rigid registration folders contain 6 folders and a summary text file:

    **Note**: Offline - Moco Fused Velocity - Rigid - contains the dual-Venc PC MRI data 
      Offline - Screenshots – Rigid – contain montages showing image registration pre and post registration 
      Summary - Rigid Co-Registration.txt – details information on Venc, Slope and Offset values

Source data

Four directories are required (per velocity-encoding direction), containing:

  1. The low-Venc modulus cine-stack.
  2. The high-Venc modulus cine-stack.
  3. The low-Venc phase-contrast cine-stack.
  4. The high-Venc phase-contrast cine-stack.

Output data

Within the nominated output directory, the following folders are created, with self-explanatory names:

  1. OFFLINE - MOCO LOW-VENC MAGNITUDE - NON-RIGID or OFFLINE - MOCO LOW-VENC MAGNITUDE - RIGID.
  2. OFFLINE - MOCO LOW-VENC VELOCITY - NON-RIGID or OFFLINE - MOCO LOW-VENC VELOCITY - RIGID.
  3. OFFLINE - MOCO FUSED VELOCITY - NON-RIGID or OFFLINE - MOCO FUSED VELOCITY - RIGID.
  4. OFFLINE - FILTERED MOCO FUSED VELOCITY - NON-RIGID or OFFLINE - FILTERED MOCO FUSED VELOCITY - RIGID.
  5. OFFLINE - MOCO FUSED VELOCITY DISCREPANCY - NON-RIGID or OFFLINE - MOCO FUSED VELOCITY DISCREPANCY - RIGID.
  6. OFFLINE - TWICE-CORRECTED FUSED VELOCITY - NON-RIGID or OFFLINE - TWICE-CORRECTED FUSED VELOCITY - RIGID.
  7. OFFLINE - FILTERED TWICE-CORRECTED FUSED VELOCITY - NON-RIGID or OFFLINE - FILTERED TWICE-CORRECTED FUSED VELOCITY - RIGID.
  8. OFFLINE - TWICE-CORRECTED FUSED VELOCITY RESIDUAL - NON-RIGID or OFFLINE - TWICE-CORRECTED FUSED VELOCITY RESIDUAL - RIGID.
  9. OFFLINE - SCREENSHOTS - NON-RIGID or OFFLINE - SCREENSHOTS - RIGID.
  10. OFFLINE - DISPLACEMENT FIELDS - NON-RIGID or OFFLINE - TRANSFORMATION MATRICES - RIGID.

Note that any older data sets lacking some of these folders will have been processed by earlier versions of the merging scripts.

There is also a plain-text summary file:

Summary - Non-Rigid Co-Registration.txt OR Summary - Rigid Co-Registration.txt.

And finally, an XLSX summary file, with detailed information grouped into several tabs:

Processing Summary.xlsx.

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