How to do Functional in Brainvoyager QX

This is based on the official Brainvoyager Quick Start Guide but edited for my needs and simplicity.

  1. Rename files to be used as “ID”_MOT
  2. Creating base FMR
    1. Open project wizard
      1. Create FMR
      2. Name file “ID”_MOT
      3. 31 Slices
      4. 70 volumes, 0 skips
    2. FMR Properties
      1. Under Referenced Protocol File (PRT)
        1. Browse
        2. Protocols (under all MOT files location)
          1. Select “Jittered MOT 2_AllConditions”
        3. Close FMR Properties
    3. Analysis Dropdown -> FMR Data Preprocessing
      1. Select Spatial smoothing -> advanced -> FWHM: 6 -> Go
      2. A video will open of motion, if it is opened with VLC Media player, it can be closed. If opened with Windows media player, save file as “ID”_MOT_MotionCorrection
      3. Right click 3D Motion Correction Parameters -> Save snapshot of plot -> Name file as “ID”_Snapshot
      4. Left click 3D Motion Correction Parameters -> Save Data -> Name file as “ID”_MOTIONDATA
  3. Coregistration
    1. Open original anatomy ISO.vmr
    2. Under 3D volume tools -> Full Dialogue -> Coregistration tab
      1. Under FMR -> VMR
        1. Select FMR
        2. (Under ID_MOT folder) Select file with longest name
        3. Select Align -> Source options -> Use AMR
        4. Fine tune -> Options -> Full -> Go
  4. Create Video Time Course
    1. Open TAL anatomical
    2. Under analysis dropdown -> Create Video time course
    3. Files for each drop down (Select to TAL after step one):
      1. First browse option select the longest titled MOT
      2. Second browse option select (Under MOT folder) IA
      3. Third browse option select (Under MOT folder) FA
      4. Fourth browse option select (Under anatomical folder) only file it shows
      5. Fifth browse option select (Under anatomical folder) only file it shows
    4. Select options
      1. Resolution: 2x2x2 -> Ok
    5. Select Go
  5. Create Mask
    1. Load TAL anatomical
    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 -> Segmentation tab
    4. Select value range so that no gray matter is selected
    5. Options -> Define VOI -> name file ID_TALMASK
    6. VOI analysis -> options -> VOI function
    7. Under create MSK -> Select use selected -> Resolution: 2 -> Create mask
    8. Save as “ID”_TAL_MIRRORMASK


I haven’t gotten around to finishing this but I will as soon as I process functional data again.

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