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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:
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
- From Sita: Andre said that in the amount of time we have for the Wed slots, the mef scans might be a bit noisy and he suggested the multiple TE scans with 3 flip angles would be better if we wanted a T2star map.
From Sita & Jean: Jean and Sita have been collecting multiple TEs intead of multiecho because of memory constraints with the 100um solenoid data. The multiple TEs still allow them to get T2* maps.
- The scans in the mef folder are not actually multiecho - we are just collecting multiple TEs to get around the memory limit and we need a high bandwidth to do so, so that also differs. These are used for the T2* mapping. The scans in the sef folder are also single echo and have the same TR but we can get a lower bandwidth which has given Sita and Jean better data for PD and T1 mapping.
- From Jean: we don't necessarily have to collect sef going forward however more cases probably have sef data as a default and so if we are doing a study and want consistent scan data, sef may still be good to collect.
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.
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: https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoScanning#UninitializedError