CAMRI:HowToScan: Difference between revisions

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== About CAMRI's Siemens Scanners ==
== About CAMRI's Siemens Scanners ==
The BCM CAMRI has 3 whole-body 3T Siemens Magnetom Trios, labelled 3T-3, 3T-4 and 3T-5.
The BCM CAMRI has 3 whole-body 3T Siemens Magnetom Trios, labelled 3T-3, 3T-4 and 3T-5.
 
3T-3 and 3T-4 currently have 8 receive channels, 3T-5 has 32 channels.
 


== Misc Notes ==
== Misc Notes ==
 
=== Slice Ordering ===
= Slice Ordering =  
3T-5 with the 32-channel head coil.
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
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.
   1, 3, 5, 7, etc.
Line 21: Line 18:
   2, 4, 6, 8, etc.
   2, 4, 6, 8, etc.
   1, 3, 5, 7, etc.
   1, 3, 5, 7, etc.
See Krista to have your badge activated.


== More details on the BCM scanners ==
== Visual Stimulus Displays ==
#Stimuli on the 3T-5 are displayed on an LCD screen. Link to manual here: [[Media:CRS_BOLDscreen_UserGuide.pdf‎|Cambridge Research Systems BOLD Screen User Guide]]
3T-3 and 3T-5 display visual stimuli on direct view LCD screens. Link to manual here: [[Media:CRS_BOLDscreen_UserGuide.pdf‎|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:
The BOLDScreen has a built-in color profile that can make images appear too dark. Instead, use the default color profile as follows:
# On the Mac laptop stimulus computer, Click on the Apple, Open "System Preferences"  
# On the Mac laptop stimulus computer, Click on the Apple, Open "System Preferences"  
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Now, desired intensity levels will be mapped appropriately to the screen.  
Now, desired intensity levels will be mapped appropriately to the screen.  


== Response Recording ==
Responses are recorded with a fORP system. Link to Jung Hwan's user guide here: [[Media:ButtonBoxConfiguration_MSB1.pdf‎|fORP Configuration]]
Responses are recorded with a fORP system. Link to Jung Hwan's user guide here: [[Media:ButtonBoxConfiguration_MSB1.pdf‎|fORP Configuration]]
For Beauchamp Lab experiments, do the following:
# Push in fORP front button
# Go to changes modes, select YES
# Select Autoconfigure
# Scroll down to HID NAR BYGRT, Select
# Confirm that Mode is 002 in top right of display
This gives a trigger as a T rather than a 5. An extra step needs to be taken to make sure that the right USB device is selected in Matlab (from the three possibilities).
To access pulse sequences, Click on Ctrl-Esc and select the "Advanced User" program. Type in the password (meduser1). Then go back, and open a Windows Explorer window. The pulse sequences are located under
  C:/medcom/mricustomer/seq
The diffusion vectors are stored in the file
  DiffusionVectors.txt


If the real-time is not working, make sure you are using the correct pulse sequence (VB17rt EPI). Also check the tabs computer (MacPro):
#Change user to admin_local
  $ su admin_local
# Kill afni:
  $ kill -9 'cat /Uses/tabs/tabs/var/afni.pid'
#If that does not help reboot tabs
#You can check the log on the scanner for hints:
  Type logviewer from the command prompt.


Image information in Trios:
Image information in Trios:

Revision as of 14:15, 24 July 2015

Brain picture
CAMRI




About CAMRI's Siemens Scanners

The BCM CAMRI has 3 whole-body 3T Siemens Magnetom Trios, labelled 3T-3, 3T-4 and 3T-5. 3T-3 and 3T-4 currently have 8 receive channels, 3T-5 has 32 channels.

Misc Notes

Slice Ordering

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.

Visual Stimulus Displays

3T-3 and 3T-5 display visual stimuli on direct view LCD screens. 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:

  1. On the Mac laptop stimulus computer, Click on the Apple, Open "System Preferences"
  2. click on "Displays", select the "Color" Tab
  3. Select the "Color LCD" profile for the second display (the BOLDscreen)

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.

Response Recording

Responses are recorded with a fORP system. Link to Jung Hwan's user guide here: fORP Configuration


Image information in Trios: 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


More stuff on real-time:

  1. Register subject, open Patient Database
  2. Find subject, click on MP-RAGE first, "Send to TABS"
  3. Once AFNI is up, then run rt fMRI sequence (look on "Special card" )
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