scanner
L1-b /usr/g/w/MRst (as genesis), or how to force the scanner to bootsometimes the scanner gets hung on mounting things, or just is generally not happy. By hitting the L1 button on the left of the console and 'b', you can force the scanner into a prompt. You can then login manually, as a typical UNIX system. as user genesis run the /usr/g/w/MRst command. This will bring up the plasma buttons that everyone knows and loves...
emergency buttons
everyone should know what they all do, but specifically: there are three that are directly connected to the signa machine in one way or another. two on the front of the bore, and one on the front of the console. these three do the exact same thing. they trip the first signa cabinet in the machine room. that brings down all associated signa equipment, including console, etc...
the other two buttons are on the walls inside the magnet room, and inside the machine room. they also perform the same thing. they trip the main circuit breakers on the wall inside the machine room, which brings down the entire room, including the pump, and other crucial things...
DAT stuff
well...our DAT drive sucks. its old. its completely imcompatible with the rest of humanity...what else? you can look at the man page for 'mt' for more hints. 'mt offline' ejects the tape smoothly. if you reboot signa while there is a tape in there, it doesnt like it too much. you will probably need to do a hard eject, from the front of the DAT drive. this will most likely 'corrupt' the tape if its a GE-signa tape. i put corrupt in quotes, because i havent seen a time yet when we couldnt recover it. there is another how2 page on that...i might expand here more later, maybe about devices, but i tire...
changing protocols w/o losing your prescription
now i have kept this one a secret mainly because it is too damn easy to do, yet seems impossible! :) like most magic...anyways. the reason that the signa will erase your prescription is because it is imcompatible with the series you are running. when you choose another protocol, it usually first kicks into a sagittal, which is not how we take our functionals (which is the only time we wanna do this). if you cancel out again, it jumps to the next series in the protocol, which is usually axial. thats pretty much it. i hit cancel and RXahead, until i am in a series that has similar enough parameters as the original you prescribed off of. then it doesnt have to erase...
APD errors
contrary to popular belief, i do get them as much as anyone else. i just dont bitch about them too much. the two most common are: failed to create header (or something like that) and recon host terminated. these are two very different errors. the first one is not serious, the second one is. when the recon host terminates, you need to restart APD2 (not the computer, just the program). choose 'quit apd2' from the menu, and type 'fp' in an xterm. it will run cleanup and start APD2 again. for the header problem, i suggest: try hitting 'scan setup' three times. if you get it each time. try reopening the database three times, if STILL you get it. try a different /apd disk. i have never had the problem go further...
THE signa software error
this is very scary looking. you get a huge window that pops up across the entire console. i didnt think it possible. this means that someone filled up the disks too much. you must reboot signa, or you will crash it (trust me). make sure that you report this to EVERYone, as it can be hacker related...
Hard reboot via the breakers
when you abuse the system as much as i try to, occasionally all hell breaks loose. i have seen signa hung. you cant login via telnet, and you cant use the plasma screens. its just not happy. time to flip breakers. these are in the first GE cabinet in the machine room. near the bottom. i usually go with the last one on the bottom left first. system cabinets(i think). flip it off for 5secs, then back on. then for good measure, i usually reset the operator console in the same way...if that doesnt do it, run away.
UNIX
xhostxhost allows you to pop up graphic windows on your current machine, when you are telnet'd into another. for instance, i am sitting on ella in the scanner room, and telnet'd into autarch to run SPM. SPM cant open windows on ella (the machine i am staring at), until i give it access. type "xhost + ella". if you type 'xhost +' you leave yourself open to all sorts of unsavory hacking attempts (i got a couple of stories i could tell...)
setenv
so many cool reasons to use this one, but i will not flex my inner geek. usually partnered with the xhost command, you need to tell the remote machine where you want to pop up windows. of note, Roger and I (mostly Roger) discovered that if you telnet into autarch. it sets your display to a hokey autarch something or other. you should explicity set it to the IP address of the machine you are staring at. oh yeah, setenv means set environment (variable). DISPLAY is the one you will probably use most my unix newbies. the command:
'setenv DISPLAY 128.97.134.45:0.0' of course replacing flora's IP address with whatever machine you are on...
foreach
unfortunetely the man page for this is just to damn silly. foreach is nice for doing tons of stuff in a serial fashion. and its only a bit like programming. here is a simple example:
commandline> foreach f (*) ##this says set f to equal everything in the current directory
foreach? cd $f; gzip foo*; cd .. ##this says take the first f, and cd there, then gzip foo*, and go back up
foreach? end ##this says you are done, and to repeat with other things equal to f
man
you dont know how much unix i have learned from man pages. these are essential, if you wanna be friendly with unix. you could learn a ton just from doing 'man ls'. you know nothing about the command. trust me. dont be scared.
apropos
similar to man, this allows you to find commands you dont know at all. apropos only works on some of our machines, but porkpie is one of them. this is a search engine. type 'apropos
backgrounding
unix is multitasking. thats why it was created. you can put any command in the background, or bring it back to the foreground. to put a command in the background, stick an ampersand after it (&). if its already running, hit cntrl-z, and then type 'bg' and that will background it. typing 'fg', will bring it into the foreground again...
grep and '|'
grep i think stands for grab expression...you can look at a file, and pull out lines that match a certain string; 'cat
MAC stuff
file size in NIH Imagethere are a handful of files that we import into NIH Image, i usually forget half of them myself:
17 slice buchar: 640x512;8bit
16 slice buchar: 512x512;8bit
qHR from SPM: 64x64;16bit
rmean from SPM:79x95x91;16bit
26 slice bshort:512x512;16bit;swap bytes
27 slice bshort:640x512;16bit;swap bytes
.MR file: usually 256x256;offset 7904;16bit
printer atrocities
throw the damn thing away.
General Lab stuff
cleaningoh what can i say. people are pigs. threathen them often. just wanted to let you know i feel your pain.
consent forms
for the two years that i was here, there was less than no organization. at this point, we have the last two years somewhat sorted,signed, and ordered in the file cabinet in the machine room. newly used forms are in the bins in the back of the console room. we need a copy of anything that anyone signs in order to be scanned here. lots has changed in the last couple of weeks with IRBs. so i will update this when it settles...maybe...
laundry
get leona and the cart. i usually get 8 bundles of bath blankets, 8 bundles of flat sheets, 4 bundles of pillow cases, and hopefully 1 bag of elusive laundry bags. keep an eye on the schedule, laundry dissappears quickly. i usually hide some extra blankets...they run out quickly (people use 3,then throw them all over the place)
paradigm files
i am collecting them. you can get to a lot of Susans' in my home directory ~fws/dotp/
this has the language mapping ones, plus a good number of others from her collaborations...
conference room enet
there is one working port in the conference room, it is in the front of the room, under the screen. there are four there, its either the top left of bottom right, i think...
Sys Admin
chmodthis command solves more system administration problems, than all others combined. whenever i get a problem, the first thing i will check is permissions, that is more than likely the source. i generally help people perform their chmod, rather than to it as root for them. the man page on chmod is downright fasinating. some quick hints. there are two ways to do it, numbers and letters. numbers are easier to do, but harder to remember. 755 makes owner do anything, and group and other can read, and excute but not write. you can also to 'g+w' which adds group write permission. these are the two most popular ones...
matlab daemon
when you reboot porkpie, you need to restart the license manager for matlab. someone will remind you, most likely zeineh(since i know he will be here another year). this is done in /pp/h/matlab5/etc. the command is lmstart. there can be problems with permissions here. its easiest for the same person to do it everytime...or root.
mounts
ugh. i am sorta lazy sometimes, and everything is not auto-mounted on every machine. man page can help here, but also look at the syntax from the /etc/fstab for hints. Alphas,SGIs and Suns differ here. umount will unmount...
accounts
GUI and commandline. GUIs are just becoming too good to pass up at this point. both Digital UNIX and IRIS have nice options. try dxaccounts in Digital and sysmanager in IRIX. more later...
core files
these take up a whopping amount of space after a while...although i have instituted a limit core size with most new accounts. occasionally i do a find for core files and remove them. beware of what should be called 'the scheding trick'... find core, rm *...DONT USE THAT.
more sooner or later...
this page no longer maintained by me