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In 2008/2009, Jean began scanning weekly in bay 5 on Wednesday evenings. RA, Sita Kakunoori conducted the majority of these scans.

While most scans were done for the MTL project, some scans may have been for other projects such as the Alzheimer's project, OCT project, etc.

MTL scan protocol

The protocols to scan are under two folders: solenoid_small_mtl_mef and solenoid_small_mtl_sef.

400um localizer 1:49
100um sef flash10, 20, 30 1:32:13 each
x 3 runs = 13:49:57 total scan time (including localizers, SNR, AFI)

100um "mef" flash10, 20, 30 TE16 1:32:13 each
100um "mef" flash10, 20, 30 TE24 1:32:13 each
100um "mef" flash10, 20, 30 TE32 1:32:13 each
= 13:49:57 total scan time (1 run for each flip/TE combo)

~28 hours needed to do both sef and mef

The actual naming convention of the scans is:


multiple TE

In addition to flip 10, we would collect flips 20 and 30 for the above 3 scans/TEs. This should be a total of 9 runs (3 flips x 3 TEs).

Reasoning behind protocol




Coil Setup

Sita sometimes has to tilt the coil in the scanner for smaller samples. When the samples aren't large enough to be wedged in the falcon tube, they float to bottom of the tube. Tilting the coil will bring it back towards the top of the tube which is the ideal spot (close to the coil turns). Tilting is easy to do now with the wooden adaptor we have there to hold it in place.

**If you have to tilt the coil, you may have to make the FOV larger to include the entire sample which will make the scans longer. You could also rotate the FOV to fit the sample and keep the same amount of scan time if doing the former will put you over your time limit.

Possible errors

Unfortunately, the protocols use Andre's buggy sequence so be careful not to let the scan queue get larger than 20 items. Sita has tried to set up the non-buggy one but it won't allow her to choose the same parameters they've been scanning with. (These are in the sef folder as mef10_150um_6e_fixlater and flash10_hires_100um_fixed). You can feel free to give this a shot or call Andre for help with it but I'm not sure if he'll be available (and he would have to do it again after the scanner upgrade so it's not in his best interest to spend time on it now). Be aware though that limiting the queue to 20 items is not a definite way to avoid the error. It seems to help but it is not a sure thing. If you encounter the error, please see the troubleshooting steps here:

JeanWednesdayScans (last edited 2021-09-22 09:44:22 by DevaniCordero)