There are three ways to save the data that you have collected at great expense. CAMRI does not back up data. Users are responsible for saving their own data!
Method 1 (Easiest): Use the Flywheel Server
Please click on the Flywheel tab above or go to https://openwetware.org/wiki/CAMRI:Flywheel for further instructions on backing up data using that resource.
Method 2: Use Box
This requires that your lab have a Box account; contact Dave Lee (email@example.com) to obtain one.
Method 3: Burning a Backup Disk
Human Subjects Protection
To scan at CAMRI, approval from your home institution institutional review board (IRB) or committee for the protection of human subjects (CPHS) is required. Click here for an IRB proposal template.
MRI Data Analysis
Updated scanner 5 to new computer and imager. Still running at VB17 software.
To schedule or cancel time on the scanner, you must use use the iLab web site https://bcm.corefacilities.org/service_center/show_external/3684 Click here for detailed instructions.
About CAMRI's Siemens Scanners
The BCM CAMRI has 2 whole-body 3T Siemens Scanners labeled 3T-4 and 3T-5.
Scanner 3T-5 is a Magnetom Trio that has a 12 channel and 32 channel head coils, Spine coil and flex body coils.
Scanner 3T-4 is a Magnetom PRISMA Fit with a Head/Neck 20 channel, Head/Neck 64 channel, Spine 32 channel, Flex 4 Large, Flex 4 Small, and body coil.
More information about the difference between the coils can be found here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3538896/
Both scanners have a bore inner tunnel diameter of 60 cm.
Report all issues to firstname.lastname@example.org
There are a few helpful videos that you can watch on YOUTUBE that will help you become a little more familiarized with our systems here at CAMRI. Here are the links: https://www.youtube.com/watch?v=pi1OLUflhTU
The sequence of operation is important so make sure it is done in this order.
Responses are recorded with a fORP system. Link to Jung Hwan's user guide here: fORP Configuration
Bold Screen Setup
For Scanner 5 Bold Screen Setup: Media:Scanner5.docx
For Scanner 3 Bold Screen Setup: Media:Scanner3.docx
Visual Stimulus Displays
3T-3 and 3T-5 display visual stimuli on direct view LCD screens.
3T-3 uses a [24" display with resolution of 1920x1200]
Link to manual here: Cambridge Research Systems BOLD Screen User Guide The BOLDScreen has a built-in color profile that can make images appear too dark. Instead, use the default color profile as follows:
Ricky Savjani has redone the gamma calibration on the 3T-5 BOLDscreen, this can be accessed in PsychToolbox as follows. First, Click here to load the table
% load in the gamma table load CRS_32BOLDSCREEN/gammaTable_Spline_fit.mat % after opening a window, call this to load the load the gamma table to to your Screen Screen('LoadNormalizedGammaTable', win, gammaTable2*[1 1 1]);
Now, desired intensity levels will be mapped appropriately to the screen.
Rough calculation of image size in degrees of visual angle: roughly 76.5 cm from screen to eyeball height of screen is 13.7 in = 34. 8 cm width of screen is 34.8 * (1024/768) = 46.4 cm atan(23.2/76.5) = 0.29 rad = 16.6 degrees ~30 degrees full width
This ppt describes the units when you draw an ROI on the relCBV map (BW). You cannot draw on the Perfusion Color map the units are not scaled.
Weekly QA scans are performed on both the Prisma and Trio scanners. Below are the results of the previous 52 week EPI QA runs.
Sequences to Use
What pulse sequence to use for fMRI
There are a variety of different pulse sequences that can be used for fMRI, including the standard Siemens EPI product sequences; multi-band EPI sequences from MGH and Univ. of Minnesota; and spiral sequences implemented by David Ress.
Here is another analysis of the same data by David Ress. The results are similar, with the G2, MB2 version winning by around 15% in fSNR over the product sequence. But, the shorter TR will also net you an improvement of ~5% in CNR in a similar length run. It is also interesting, however, that the G3 run had less aliasing artifact, suggesting that shorter acquisition times reconstruct more cleanly.
Similar results were obtained with a phantom:
What T1-weighted Anatomicals to Use
Most studies collect at least one scan with structural contrast in order to align their other runs (functional, DTI, etc) to other participants and to published atlases. In some cases, measurements such as volume or cortical thickness are also derived from these scans. We have tested a few of these on the Prisma (Bay 4) and will run similar analyses on the Trio (Bay 5) soon. CAMRI (specifically, Meghan) recommends the following scans for new studies, and can easily set these up in your protocol:
(1) 1mm isotropic scan. Acquisition time: 4:01. Contrast to noise ratio (CNR): ~2.0. This is a good choice if speed is of the essence, and your main goals are alignment of lower-resolution scans.
(2) 1mm isotropic scan. Acquisition time 5:12. CNR: ~2.6. High quality T1 scan that will suit most studies. Very good CNR.
(3) 800um isotropic scan. Acquisition time: 6:38. CNR: ~2.2. A happy medium between speed and resolution.
(4) 700um isotropic scan. Acquisition time: 8:18. CNR ~ 2.2. Based on the HCP sequences. This is recommended if your study would benefit from higher resolution. For instance, if you plan to do cortical thickness studies or are interested in segmentation of fine structures, this could be a good choice.
A note on CNR: This was calculated from only a handful of people (sometimes, just from one participant). CNR was calculated using FreeSurfer segmentations of the cortical ribbon and the white matter mask. CNR=(Mean(white) - mean(grey)) / mean(std(grey), std(white)). Signal was taken from the raw image, with prescan normalize turned ON.
David Ress' former student Andrew Florens examined the acquisition time stamps and found that axial slices are collected from Superior to Inferior (head to foot). If an odd number of slices is acquired, the slice order is
1, 3, 5, 7, etc. 2, 4, 6, 8 etc.
If an even number of slices is acquired, the slice order is reversed:
2, 4, 6, 8, etc. 1, 3, 5, 7, etc.