3T MRI lab How to notes

Please bera with us. This set of lab notes is now somewhat out of date. No serious revision is planned until we start up a new lab expected in fall, 2005.

This page offers a series of lab notes that are specific to the operation of the UCLA 3T MRI Research Lab.
If you want to become Fred, click here. If you would like to submit your own paragraph, e-mail Fred or Mark.

You can also find General Instructions for downloading program source files.

Some of these tools are now available in executable form for distribution. Here, you can download Apple OS/X versions or Sun/Solaris executables.
Repairs Scanning Logger Image Processing Utilities Computers Oldies
In thinking about your questions, consider looking at these pages for examples or artifacts from known sources
Wayne Patola's MR Artifacts and Mark Cohen's MR artifacts

Repairs

How to Build your own MR-compatible button box for the 3T lab. [Dec 11, 2003]
How to Trouble shoot the AV system [Sep 7, 2000]

Scanning

How to Present Stimuli in the 3T lab [Dec 15, 2003]
How to Scan - The Cannon Lab Guide [Aug 7, 2000]
How to Assess scanner stability using P2P. [Jan 13, 2001]
How to Get the maximum number of slices per TR. [Aug 21, 2000]
How to Select the flip angle to use for functional or gradient echo imaging. [Sep 4, 2000]
How to Find the AC-PC line. [Aug 21, 2000]
How to Perform a Dynamic Orbit Scan. [Jun 5, 2001]

Experiment Logger

How to Log in to the Experiment Logger
How to Enter Patient info
How to See how many scans remain on your protocol [Feb 19, 2001]

Image Processing

How to Create a T2 Map [May 20, 2006]
How to Install OS X Tools: Summary and Installation Instructions [Jan 13, 2004] NEW - (X)MedCon tool for Panther added. [ May 10, 2004 ]
How to Determine the volume of brain lost in merging multi-subject data sets [March 18, 2003]
How to Create a Synthetic Time Series for testing statistical programs [Feb 26, 2003]
How to Convert between file formats using imconvert. [March 6, 2003]
How to Automatically hunt for artifacts with 'Outlier'. [Jan 11, 2001]
How to Select, extract or reorder slices using a modified version of imconvert [April 16, 2003]
How to Average the responses from Event-Related trials. [Nov 19, 2002]
How to Normalize image intensity using EQ. [Jul 5, 2000]
How to Convert Signa 5.x time series to local formats for analysis [Dec 10, 2001]
How to Do basic single subject analysis. [Nov 29, 1999]
How to Change to and from analyze 3D files and genesis files. [Sep 11, 2000]
How to Setup your data for processing with AIR. [Nov 29, 1999]
How to Use SPM - the Official manual [Jan 3, 2000]
How to Use SPM (a basic brain mapping guide) [Jan 3, 2000]
How to Use SPM (the Cannon Lab Guide to SPM) [Sep 4, 2000]
How to Do subject-subject registration & Create Your Own Atlas [Woods Dec 9-1996]
How to Extract a table from SPM. [Sep 20, 2000]
How to Extract an eigenvariate time course from SPM. [Sep 20, 2000]
How to Get started with AFNI. [Mar 21, 2000]

Utilities

How to Reverse the anatomical order of slices in a volume. [Apr 17, 2002]
How to Test image stability using P2P. [Feb 4, 2004]
How to Edit or create the contents of an analyze image header. [Dec 28, 2002]
How to Show the contents of an image header. [Nov 25, 2001]
How to Make an APD Backup. [Mar 9, 2001]
How to Compress files using SmallTime. [Oct 20, 2000]
How to Test for RF leaks. [Nov 9, 1999]
How to Test devices for added system noise. [Nov 9, 1999]
How to Retrieve data from CD or tape. [Mar 3, 2000]
How to Swap time and z axis in an Analze header [Nov 25, 2001]

Computers

How to Do some basic unix. [Jun 27, 2005]
How to Understanding UCLA file formats. [Sep 9, 2000]
How to Maintain accounts on the BMD Logger [Sep 9, 2000]
How to Update the Matlab license file [Sep 9, 2000]
How to Reboot a Sun computer from CD. [Aug 24, 2001]
How to Video Output-Switch Between MAC and PC [Apr 11, 2002]
How to Learn some basic ssh commands [Nov 14, 2002]
How to Use ssh - examples [Nov 14, 2002]

Old Guys

How to Reset the Signa database in the case of extreme corruption. [Jun 1, 2001]
How to Recover from SI error: "please check the path /usr/g/mrraw/HEADER_POOL". [Sep 20, 2001]
How to Restart the APD system from the login screen. [Sep 4, 2000]
How to Recover from a bad shim. [Nov 2, 1999]
How to Reboot the recon host (when prompted). [Mar 24, 2000]
How to Clear /usr/g/insite/tmp when full. [Nov 9, 1999]
How to Perform offline reconstruction of EPI data. [Mar 24, 2000]
How to Change control variables (CV's). [Mar 13, 2000]
How to Reconnect the microphone on the Macintosh. [Nov 9, 1999]
How to Shorten APD file names for CD and Macs. [Oct 19, 2000]
How to Login to the Signa. [Aug 21, 2000]
How to Adjust the Signa image intensity [Feb 28, 2000]
How to Get an xterm on the Signa. [Aug 21, 2000]
How to Construct a 100baseT cable. [Mar 16, 2000]
How to Extract images from the Signa using ximg. [May 18, 2000]
How to Backup and restore the Signa. [Sep 13, 2000]
How to Recover a damaged DAT tape. [Oct 19, 2000]
How to Re-boot the signa. [Dec 16, 1999]
How to Fix the AV system. [Nov 9, 1999]
How to Build your own brain. [Nov 9, 1999]
How to Minimize ghost artifacts on the EPI system. [Nov 9, 1999]
How to Scan (according to Roger and Nancy. [Nov 9, 1999]
How to Setup for a Real time scan. [Nov 9, 1999]
How to Disable motion of the patient table. [Nov 29, 1999]
How to Change the APD scan disk. [Nov 9, 1999]
How to Scan (1) [Nov 9, 1999]
How to Scan (2) [Nov 9, 1999]
How to Restore data from a CD. [Nov 9, 1999]
How to Reset the shim. [Nov 9, 1999]
This page was reconstructed by MarkCohen on 3.18.03