xtracting Images from the GE Scanner (ximg)

Brain Mapping Center

Extracting Images from the GE Scanner (ximg)

Overview.

This tool is used to extract conventional images from the GE console.
Note: this is not for EPI scans of any type.

Before you begin extracting images, check the Scanner Schedule to make sure no one is using the scanner: http://airto.hosted.ats.ucla.edu/~MRCalendar/3tmri.html

You may also see if anyone is currently logged in by using http://airto.hosted.ats.ucla.edu/cgi-bin/ShowMRUser

** YOU MUST NOT EXTRACT IMAGES WHILE INVESTIGATORS ARE SCANNING**

Function: Type: Notes:

Get a terminal on the Signa Remote login for transfer is no longer allowed

Change to the transfer directory cd /usr/g/insite/tmp

df .

Make sure tmp is not full. You must remove any images you place there as soon as possible, ideally right after copying them to a remote directory. If there are already scans in this directory, you may need to extract one series of the scan at a time (see instructions below), or check with Fred Sabb to see if scans can be removed. DIRECTORY CAPACITY MUST BE LESS THAN 90% AT ALL TIMES!
Fill this up and you crash the scanner!

run extraction tool: ximg -n Allows you view list of scans still on scanner (follow menu options). If the scan you wish to extract does not appear in this list, it may have been removed and stored to DAT. Contact Fred regarding access to DAT storage and restoring scans to the scanner.

Example:
ximg -i E1234Sall -t -s Numbers indicate Signa (scan) number; S denotes series (all for each series run); -t puts images in standard" or GE format
-s ensures that the demographic information is captured

Example:
ximg -i E1234S3Iall -t -s If you wish to extract only one series of scans, indicate which series after S followed by Iall

file transfer protocol: ftp your.machine.edu FTP from /usr/g/insite/tmp

prompt, bin, mput E1234*

Clean out tmp directory! rm /usr/g/insite/tmp/E1234* Leaving your scans in this directory can hinder the next person trying to acquire data on the scanner. DIRECTORY CAPACITY MUST BE LESS THAN 90% AT ALL TIMES!! Fill this up and you crash the scanner! (yes, really)

For problems related to image extraction, contact Fred (64364) or Mark (65437).
Thanks to Laurie Carr for the write-up

Back to HowTo pages

This page is maintained by Fred Sabb [updated 09.13.00 by MSC]

Function:	Type:	Notes:
Get a terminal on the Signa		Remote login for transfer is no longer allowed
Change to the transfer directory	cd /usr/g/insite/tmp
	df .	Make sure tmp is not full. You must remove any images you place there as soon as possible, ideally right after copying them to a remote directory. If there are already scans in this directory, you may need to extract one series of the scan at a time (see instructions below), or check with Fred Sabb to see if scans can be removed. DIRECTORY CAPACITY MUST BE LESS THAN 90% AT ALL TIMES! Fill this up and you crash the scanner!
run extraction tool:	ximg -n	Allows you view list of scans still on scanner (follow menu options). If the scan you wish to extract does not appear in this list, it may have been removed and stored to DAT. Contact Fred regarding access to DAT storage and restoring scans to the scanner.
Example:	ximg -i E1234Sall -t -s	Numbers indicate Signa (scan) number; S denotes series (all for each series run); -t puts images in standard" or GE format -s ensures that the demographic information is captured
Example:	ximg -i E1234S3Iall -t -s	If you wish to extract only one series of scans, indicate which series after S followed by Iall
file transfer protocol:	ftp your.machine.edu	FTP from /usr/g/insite/tmp
	prompt, bin, mput E1234*
Clean out tmp directory!	rm /usr/g/insite/tmp/E1234*	Leaving your scans in this directory can hinder the next person trying to acquire data on the scanner. DIRECTORY CAPACITY MUST BE LESS THAN 90% AT ALL TIMES!! Fill this up and you crash the scanner! (yes, really)