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Scanning Protocol MC4
Operating Software: PV6
Operator Profile: Dan
Coil: Cryo
Manganese: No
Gado: No
Bed Setup: Cryo insert bed with bruker beige nose cone and toothbar. Black foam neck cone is inserted right in front of the nose cone and secured to the bed with double sided tape. Both strips of long gray foam are placed on the bed floor after the black foam neck cone. Next comes the respiration pillow, taped on the gray foam pieces, just after the foam neck cone. Dex shunt is placed IP, and mouse’s rear is taped down, as far up the mouse as possible without the tape band interfering with the coil.
Heat Setup: Heated air pump with thermometer in green tube hole. PC sam heat set at 40C, “on/off with PVM max heat” option, set to 30.7%. Green tube fed through the semi-circle of the bed.
Anaesthetics: Iso/Dex combo. Induction at 3.5% iso until the mouse is out of it. Then bolus injection of 1:60 dex based on weight (see MC4 injection sheet in scanning box. Then the mouse is returned to the induction chamber at 2% iso for another two minutes or until it is out of it again. Mouse is transferred to the scanner at maintenance of 1.5% iso and is stepped down periodically to 0.3% iso over course of scan (see below). 1:60 dexmedetomidine continuous injection starting at 10 min post bolus during scanning, also based on weight. Continuous injection delivered in 3 ml syringe with injector set at diameter 8.66 mm and units in ul/hr. High respiration is to be ignored.
Air mix: 20% O2, 80% air. To achieve, set O2 at 0.232 L/min, and air (while run through an O2 meter) at 0.755 L/min.
Default reconstruction parameters: 16 bit signed, absolute, magnitude
Scan templates location: mouse/head/anatomy/mc4
Exported scan types: raw
MCH_MC4_001_001_1
[Mallar’s lab][Megan’s project code][cohort][subject number][timepoint]
-4(ish) m Isoflurane induction at 3.5 % begins.
0.0 m Mouse is removed from the box, given bolus injection of dex indexed to weight, returned to box at 2% iso and timer starts.
2.0 m Box is disconnected from iso machine, mouse is brought to scanner and placed in bed at 1.5% iso. Dex shunt is placed IP in mouse, but not turned on yet.
10.0 m Dex continuous injection begins through shunt and auto-injector. Injection rate is also indexed to weight of mouse.
20.0 m Iso is reduced to 1.2%.
25.0 m Iso is reduced to 0.8%.
30.0 m Iso is reduced to 0.5%.
35.0 m Iso is reduced to 0.3%.
45.0 m Minimum time has elapsed, and EPI may now start.
- New study. Set up scan exam card with mouse name and project code.
- Click and drag the “mc4” folder into the exam area. Mouse/head/anatomy/mc4.
- Tripilot. Run the tripilot scan with “continue”. Readjust mouse in the scanner as necessary. If you have to redo, duplicate the triplot, and remember to go into “instruction” and select “all setup and acquisition” to ensure the new triplot redoes all the setup measurements.
- Enter the adjustment menu on the ADJ BO MAP scan, do not run this directly. Here you will...
- Wobble, running with “setup”. Remember that PV6 is backwards and does channel 2 (90 degrees) first.
- Set the reference power. Thin the slab to 1mm and flip to coronal. Position inside the top of the brain. Run with “start”.
- B0 map. Select the B0cur option in the adjustments. Ensure the big square contains the whole brain, but otherwise don’t bother too much with planning. Run with “start”.
- The skip. Exit back to the scan list and select the structural scan. Hit skip, and the B0 map will be passed over.
- Plan the structural scan shim. Note: this scan has a shim built into it, that will use the previous B0 map. Go to geometry, and select shim instead of slice package, and highlight index 1. Stretch and move the oval to be inside the brain, but cover most of it.
- Plan the structural scan FOV. It’s easy to miss this step with all the excitement of planning the oval shim. Select the slice package in geometry and plan the fov as usual, centered in the middle of the brain. This scan has antialiasing in the up-down direction to compensate for tissue below. Run it with “continue”.
- Plan the epi scan. Drag the slices to cover the whole brain, sacrificing a bit of the olfactory bulb and cerebellum if necessary. Move the saturation pulse to just outside the bottom of the brain. It will blank out any tissue in its field. This is faster than anti-aliasing, but solves the same problem. Run with “continue”. This has a minimum start time of 45 min post-bolus, and 10 min post final iso turndown.
Structural
Type: 3D FLASH
Matrix: 258x210x128 with orientation: (rostral-caudal, left-right, ventral-dorsal)
FOV: 18.06x14.7x8.96mm
Resolution: 0.07mm isotropic
Anti Aliasing: 1.641, ventral dorsal direction
TE: 5.134ms
TR: 21.617ms
Flip Angle: 10
Averages: 1
Length: 23m54s
Slice Orientation: coronal
Read Orientation: rostral-caudal
Bandwidth: 25000 Hz
Functional
Type: 2D gradient EPI
Matrix: 70x40x26 with orientation: (left-right, ventral-dorsal, rostral-caudal)
FOV: 18.75x10x13mm
Resolution: 0.25x0.25x0.5mm
Anti Aliasing: 1.28, left-right direction
TE: 15ms
TR: 1000ms
Flip Angle: 90
Averages: 1
Length: 8m20s
Slice Orientation: axial
Slices: 26
Slice Thickness: 0.5mm
Slice Gap: 0mm
Read Orientation: left-right
Bandwidth: 300480.8 Hz
Repetitions: 500
*FOV saturation band placed under brain to prevent flipping