Beauchamp:HowToScan: Difference between revisions

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= How to Scan =
= How to Scan =
For full details, see [[CAMRI:HowToScan| CAMRI wiki on how to scan]]


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


== About the UT Philips Scanner ==
== Using the fORP ==
Our scanner is a 3 T whole-body Philips scanner with 16 parallel RF channels.
For Beauchamp Lab experiments, do the following:
It is a hybrid Intera (older) and Achieva (newer).
# Push in fORP front button
Slice acquisition is set to the default order, with the time maximized between adjacent slices. Slice acquisition order seems to be from bottom to top, based on the raw DICOM images (where the first image is the most inferior) and real-time view seen during scanning (where the most inferior images are display first, sometime most superior aren't displayed at all before the next TR starts).
# Go to changes modes, select YES
The scanner technologist (Vips Patel) will run the scanner for you.
# Select Autoconfigure
 
# Scroll down to HID NAR BYGRT, Select
== About the BCM CAMRI Siemens Scanners ==
# Confirm that Mode is 002 in top right of display
The BCM CAMRI has 3 whole-body Trios and 1 head-only Allegra (as well as a decommissioned Allegra).
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).
We usually use 3T-5, one of the Trios.  
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.
 
 
== About the BCM BOLD Screen ==
The BCM scanner has a BOLDView display.
Here is the manual for that:
 
[[Media:CRS_BOLDscreen_UserGuide.pdf‎|Cambridge Research Systems BOLD Screen User Guide]]
 


== 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
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   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 (mayor55quimby)
#Change user to admin_local  
   $ su admin_local
   $ su admin_local
# Kill afni:
# Kill afni:
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#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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