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Scanning Protocol SML
Operating Software: PV6
Operator Profile: Dan
Coil: Cryo
Manganese: Yes; Lani’s neonate dosing
Gado: No
Bed Setup (both timepoints): Cryo insert bed with Jeremie’s custom neonate 3D printed nose cone and slider combo piece slid into place. Foam neonate vice (head only version), is inserted onto the slider piece, all the way forward. Dex shunt is placed subcue.
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 semi-circle of bed.
Anaesthetics: Iso/Dex combo. Induction at 4% iso. Maintenance begins at 1.5% iso and is held constant. Half dose dexmedetomidine bolus and continuous injection starting during scanning.
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/sml
Exported scan types: raw, dicom
MCH_SML_428_001_1
*updated to include timepoint, note scans taken before Aug27th do not have timepoint
Mallar’s lab_Syrina’s project code_cage number_subject number_timepoint
*Note that when naming the study before Aug27th, sml is for first time point, sml2 is for second
*Note that from Jan 13th 2022 onwards, cage numbers in the second generation moms can have a secondary _# attached to them to note that multiple moms came from one of those original cages
0.0 m Isoflurane induction at 4 % begins. 3.5 m Mouse is removed from the box, given bolus injection of dex indexed to weight. 5.5 m Box is disconnected from iso machine, mouse is brought to scanner and placed in bed at 1.5% iso. Dex shunt is placed subcue in mouse, but not turned on yet. 13.5 m Dex continuous injection begins through shunt and auto-injector. Injection rate is also indexed to weight of mouse.
- New study. Set up scan exam card with mouse name and project code.
- Click and drag the “sml” folder into the exam area. Mouse/head/anatomy/sml.
- 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 olfactory bulb and most of the brain as possible. 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 does not have a set minimum time because the anaesthetics are more constant, and the length of the structural scan ensures a long period of stability before the epi.
Structural
Type: 3D FLASH
Matrix: 190x164x123 with orientation: (rostral-caudal, left-right, ventral-dorsal)
FOV: 17.10x14.76x11.07mm
Resolution: 0.09mm isotropic
Anti Aliasing: 1.333, up-down direction
TE: 5.37ms
TR: 26ms
Flip Angle: 37
Averages: 2
Length: 23m18s
Slice Orientation: coronal
Read Orientation: rostral-caudal
Bandwidth 29761.9 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