CAMRI:HowToScan: Difference between revisions
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== Quality Assurance == | |||
Weekly QA scans are performed on both the Prisma and Trio scanners. | |||
Below are the results of the previous 52 week EPI QA runs. | |||
PRISMA 52 Week EPI QA | |||
[[Image:QAS4.jpg]] | |||
TRIO 52 Week EPI QA | |||
[[Image:QAS5.jpg]] | |||
== Misc Notes == | == Misc Notes == |
Revision as of 13:39, 22 September 2017
Human Subjects ProtectionTo 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 AnalysisClick here for more information on MRI data analysis. Change LogNotes on Recent Changes to Our Equipment. SchedulingTo 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 ScannersThe 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. Both scanners have a bore inner tunnel diameter of 60 cm. TroubleshootingReport all issues to camri@bcm.edu http://openwetware.org/images/0/01/CAMRI_MRI_Safety_Manual.pdf 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. Burning a Backup DiskBurning a Backup Disc:
Sending Images to BoxHow to Send Images to Box: Media:Sendingtobox.docx Response RecordingResponses are recorded with a fORP system. Link to Jung Hwan's user guide here: fORP Configuration
Bold Screen SetupFor Scanner 5 Bold Screen Setup: Media:Scanner5.docx For Scanner 3 Bold Screen Setup: Media:Scanner3.docx
Visual Stimulus Displays3T-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 ASL HelpThis 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. Media:ASL.ppt Quality AssuranceWeekly QA scans are performed on both the Prisma and Trio scanners. Below are the results of the previous 52 week EPI QA runs. PRISMA 52 Week EPI QA TRIO 52 Week EPI QA Misc NotesSlice OrderingDavid 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.
What pulse sequence to use for fMRIThere 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: |