Beauchamp:HowToScan: Difference between revisions

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next step is [[Beauchamp:CreateAFNIBRIKfromMR|Getting raw data from the scanner]]
next step is [[Beauchamp:CreateAFNIBRIKfromMR|Getting raw data from the scanner]]


 
== Using the fORP ==
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.
 
== About the BCM CAMRI Siemens Scanners ==
The BCM CAMRI has 3 whole-body 3T Siemens Magnetom Trios.
We usually scan on 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
  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.
See Krista to have your badge activated.
 
== More details on the BCM scanners ==
#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]]
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"
# click on "Displays", select the "Color" Tab
# 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,  [[Media:gammaTable_Spline_fit.mat|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.
 
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:
For Beauchamp Lab experiments, do the following:
# Push in fORP front button
# Push in fORP front button
Line 66: Line 19:
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).
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).


== Accessing Pulse Sequences ==
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  
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
   C:/medcom/mricustomer/seq
Line 71: Line 25:
   DiffusionVectors.txt
   DiffusionVectors.txt


== Using Real-Time ==
If the real-time is not working, make sure you are using the correct pulse sequence (VB17rt EPI). Also check the tabs computer (MacPro):
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  
#Change user to admin_local  
Line 79: Line 34:
#You can check the log on the scanner for hints:
#You can check the log on the scanner for hints:
   Type logviewer from the command prompt.
   Type logviewer from the command prompt.
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:
More stuff on real-time:

Latest revision as of 14:21, 24 July 2015

Brain picture
Beauchamp Lab



How to Scan

For full details, see CAMRI wiki on how to scan

next step is Getting raw data from the scanner

Using the fORP

For Beauchamp Lab experiments, do the following:

  1. Push in fORP front button
  2. Go to changes modes, select YES
  3. Select Autoconfigure
  4. Scroll down to HID NAR BYGRT, Select
  5. 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).

Accessing Pulse Sequences

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

Using Real-Time

If the real-time is not working, make sure you are using the correct pulse sequence (VB17rt EPI). Also check the tabs computer (MacPro):

  1. Change user to admin_local
 $ su admin_local
  1. Kill afni:
 $ kill -9 'cat /Uses/tabs/tabs/var/afni.pid'
  1. If that does not help reboot tabs
  2. You can check the log on the scanner for hints:
 Type logviewer from the command prompt.

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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