How to do Anatomical in Brainvoyager QX

  1. Rename files to be used as “ID”_ANAT
  2. Creating the base VMR
    1. New Doc Wizard
    2. VMR -> DICOM -> name file “ID”_ANAT[.vmr]
    3. Select yes -> select ok
    4. Make sure there are 256 columns -> do not change number of slices -> select finish
    5. Select yes -> select ok -> select save
  3. Inhomogeneity Correction (Volumes tab -> “Inhomogeneity correction, V16 tools…) pt. 1
    1. Make sure the following options are set:
      1. Number of cycles: 2
      2. Trilinear interpolation
    2. Select go
    3. Using Contrast to isolate white matter
      1. Options tab -> Contrast and Brightness
      2. Adjust contrast and brightness (Turning con. Up and bright. Down respectively) until majority of gray matter is not visible.
        1. This takes multiple rounds of adjustments depending on brightness of gray matter due to scan. Between each adjustment select Ok and Ctrl+S.
        2. In case of too much white matter erased as well, select reload all.
        3. Note: If unsure contrast adjustments are saved, selecting reload all should not revert file to original brightness if successfully saved.
      3. 3D Volume tools dialogue (Volumes tab -> “3D Volume tools…”)
        1. Full dialogue -> Segmentation tab
        2. Under “Value Range” plug in random numbers for the “Min” and “Max” values (Do not change the “New”, value should be 240)
          1. Note: If using contrast adjustment method, the minimum value will most likely be under 100 and the Max value should stay 255.
  4. Once values are found, select options -> Define .voi -> Name file: “ID
  5. Region of Interest analysis -> Options -> VOI Functions -> VOI Transparency set to 1.0
    1. Under “VOI -> Draw in VMR” click convert
    2. Select Save -> Select Save -> Select Yes
  6. Inhomogeneity Correction pt. 2
    1. Select Correct IIH
    2. Select Save .v16
      1. “(Click last file in list for base file name)…”_MC
    3. To Remove Excess Skull
      1. Make copy of “’ID’_ISO_IIHC.vmr”
      2. Open copy in Brainvoyager
      3. 3D Volume tools -> Segmentation
      4. Under subsection “Draw with mouse”
        1. Check Enable
        2. Select 3D (Cube)
  7. Ctrl: draws | Shift: Erase
    2. In case of mistake, select reload all
  8. ACPC Space
    1. 3D Volume tools dialogue -> Full dialogue
    2. Under Talairach Tab
      1. Under ACPC Transformation
      2. Select Manual -> Find AC point -> Select point with crosshairs -> Select ok
  9. Select Find ACPC Plane ( Start with Z value and work up to the X value) -> Select Ok
  10. Select Transform to ACPC -> Select Go
    1. Set each point in the Talairach landmark list
  11. Once finished setting points Select Save .tal -> Save
    1. “ACPC -> TAL” -> Select go
  12. Save


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