15 T scanner

15 T data is stored here:

/autofs/space/vault_007/users/andre_hp/15T

In February 2016, Andre ran some initial tests using a new 15 T birdcage built by Azma (called InitialTestsBirdcage). There were some shifts between some of the runs and some were discarded, but initial results looked ok for 100um, 75um and 50um. Averages were created using mri_robust_template:

mri_robust_template --mov <path to all input runs> --template <output_file_name.mgh> --satit --average 0 

More runs were collected at 50um to increase SNR (I36_lh_mtl_15T), however the contrast wasn't great even with this large number of runs. It was also discovered that getting higher resolution isn't possible without changes in software (the matrix size or number of slices seems to be set to 512, and increasing it farther leads to random noise instead of images. Higher resolution such as 40um without increasing the matrix size causes too much wrapping).

The same sample (I36_lh_mtl_15T_070716) was rescanned with lower bandwidth and higher TR/TE to see if this would lead to better contrast, as evaluated by Jean. 18 runs were acquired at 50um resolution, but this didn't seem to be enough (we had to cut the scan short to put it in cryo for sectioning). The results were inconclusive, so we scanned another sample for a ridiculously long amount of time (I40_hp_15T_50um, 72 runs). The results were averaged in multiple ways (all with mri_robust_template): averaging all 72 runs, averaging every four runs (1-4, 5-8, ... , 69-72) so that motion between runs is less, then averaging all 18 of those 4run averages together, and averaging every two 4run averages together, then averaging all 9 of the 8run averages. One of the first two averages were better, but still disappointing considering the amount of scan time. Images are located here:

/autofs/space/vault_007/users/andre_hp/15T/I40_hp_15T_50um/mri/average/72runs/gre_mgh_me_as_50um_8deg_robust_template_mean_1-72_72runs.mgz
/autofs/space/vault_007/users/andre_hp/15T/I40_hp_15T_50um/mri/average/72runs/gre_mgh_me_as_50um_8deg_robust_template_mean_A-R_72runs.mgz

It seemed that even with high SNR (from 72 runs) using a sample with good contrast (I40 has good MR contrast in hemi and 7T solenoid scans), the contrast and structures Jean was looking for weren't apparent. We decided to try lower resolution scans with different TR/TE values to get a better idea of what parameters to use to get good contrast. This was done at 100um first, though the echo train and different flip angles weren't sufficient enough:

/autofs/space/vault_007/users/andre_hp/15T/I42_hp_15T_100um/mri/parameter_maps

Bruce wanted to collect lower res data (200um) with a longer echo train (8 echoes) and higher number of flips (echoes 2-30, every 2 degrees). This was acquired on the same sample:

/autofs/space/vault_007/users/andre_hp/15T/I42_hp_15T_200um/mri/parameter_maps

Higher flips seem to have better contrast, though Bruce wanted to do some optimization to see what parameters would be best. As of December 2016, Bruce wanted some gm/wm labels on this 200um data set, to see if he could do some optimization (this still needs to be done as of Feb 2017). The goal would be to find a good set of parameters to use for higher res scans, and not to continue collecting 200um data on the 15T scanner.

Since October 2016, no new data has been acquired. Andre tried to set up trufi diffusion, but ran into issues due to outdated Siemens software. Also, Andre wanted to investigate point scanning at the 15 T (which is highly inefficient but would lead to interesting results), but this required setting up streaming and using the portable RAID. Andre is still interested in pursuing these scan, so it may be worth setting up a time with him in March to try it out.

4.7 T scanner

In November 2016, we started to investigate using the 4.7 T scanner for hemi or whole brain scans. Lee met with Chris Farrar to try to set this up, but there were many issues (mostly since we have to use the largest gradient set, which nobody else uses). After discussing with Bruce, we put using this scanner on hold until we get support from the center. Here are some notes from this setup:

SmallBore (last edited 2017-04-13 23:10:40 by LeeTirrell)