New to the Lab
From Brain Mapping
Please see FAQ: Shared Resources for in depth list of available resources.
Virtually all work in the lab is done in one of three ways:
- On a group resource lab computer
- On the hoffman2 cluster
- On another lab member's computer
Let's cover each of these in detail and how you can gain access to that resource.
Group Resource Lab Computer
These are computers available for reserving by anyone in the lab. So far, we have approximately 5 of these. To gain an account on these computers, ask for the local lab manager/administrator
or shoot an email at CCN Support.
Prepare the following information:
Subject: Lab Account Request Name: Your Name Email: Your preferred email Phone: Phone Number to reach you when out of the office AIM: your aim chat account if you don't mind being reached this way
You will receive a confirmation email with any specific instructions once your account is created.
A very detailed, step by step walk through on obtaining an account on Hoffman2 is found on the Getting a Hoffman2_Account wiki page.
Please remember that all support issues, lost passwords, forgotten accounts, and more regarding Hoffman2 should be directed to the ATS Support.
Another Lab Member's Comptuer
Although it may sound wild, the only person who can help you with this is the person who owns the computer. :) Also, ask permission first.
Tools & Utilities
During the course of your work for the lab, you'll often need to perform various tasks that revolve around using image analysis software, scripting, shell scripting (bash, zsh), and use of clusters (qsub, qstat, and writing job submission scripts).
If you are working on Hoffman2, miles, or a lab computer all the utilities you need to get working are already available. If this is not the case, please send a request to
CCN Support or the local administrator requesting the program be added.
Just about any editor is sufficient. Know how to use them. More information at Text Editors. Popular Editors:
BASH is the shell you'll most likely be using in the lab and on our clusters. Knowing the shell and how to write simple scripts is absolutely essential to get your work done without suffering the ails of Repetitive Stress Syndrome. Ask around the office about Carpal Tunnel if you need inspiration to learn how to script. :)
Here are the basics:
Keeping "In the Loop"
Lab meetings, mail outs, notifications, where do they come from and how do you get them? Easy.
- The Cohen-Bookheimer Lab mailing list receives all email specific to our lab. This includes notifications of hardware issues, software updates, general notifications, meetings, filed trips, and picnics.
- The Cluster-Users mailing list receives notifications about various cluster issues and updates. These are mostly hardware related or may involve software specific to the cluster, e.g. a scheduled down time for updating FSL.
- Classes. If you're taking a course from Susan or Mark, there may be a mailing list specifically for that class. Please check with your professor for details.
Finding More Information
For further information there is one resource above all others. I'm going to repeat it 3 times (each repetition imbues the phrase with deeper meaning...I learned this from top 40 music):
- Man Pages
- Man Pages
- Man Pages
Man Pages are the be all end all of information for UNIX programs. Man is short for "Manual" or as Websters likes to chirp:
1. a book of instructions, esp. for operating a machine or learning a subject; a handbook : a computer manual | a training
And that's just what man pages do, they instruct you on all the ins and outs of how to use a specific program. Man pages are a formal language. They require a rigid format that is unambiguous and succinct in its interpretation. It's not as bad as it sounds, but may look confusing at first. Fear not! Our friendly O'Reilly members have written a tutorial on how to use the built in UNIX manuals and documentation to uncover the mystery:
- Read the F(riendly) Manpage or RTFM
It may sound funny, but Google is an amazing resource. Often simply typing in the error you receive in google is enough to find a solution.
Boolean, AND Searches
In my experience, one powerful feature of Google that many are not aware of is its Boolean search methods. By default, the AND operator is used. For example, a search for red dog is translated as "red AND dog". This means google looks for all pages that contain both the words Red and the word Dog, but not pages with only red or only dog.
Any set of words placed in quotes is taken as a literal search. For example, by quoting the above search "red dog" google finds all pages with the exact string "red dog", but ignores pages that may have red and dog at different parts of the page. The quoted string is very useful for finding information about errors.
Broadening and Narrowing Searches
The technique of broadening and narrowing searches is the most important for efficient Googling. Here are some tips:
- If you search for the word "analysis" and find nothing, try a variation of the word such as "analyze".
- Use the shortest variation of a word in your search that is still unique or pertinent to increase the number of results. For example, instead of searching for "programming" search for "program". The key here is that all pages that contain "programming" also contains "program", thus you have broadened the possible number of hits. Some other results:
- instead of scanning, search for scan
- instead of unfolding, search for unfold
- instead of boolean, search for bool
- Narrow your search with quotes
- For example, if you search for functional magnetic resonance and get far too many hits, you can narrow the results by searching for the exact string "functional magnetic resonance"
- Use acronym and synonyms liberally. e.g. MRI instead of magnetic resonance imaging
- Eliminate terms from your search that are obviously specific to your individual case.
- For example, say you get an error: "FSL Fubar Error 521: some_file_I_named.txt". Now, obviously not everyone in the world has a file named "some_file_I_named.txt". Thus, it is a frivolous search term that does little in helping google find a solution for us. Trimming this down to the terms that would be common to any error of this time produces much better results. e.g. "FSL Fubar Error 521"
AHHHHH HELP ME!!: How to Get Help
You've read the docs, you've searched google, you've read the man pages....and yet cannot find a solution. What do you do now?
First off, it's worth looking over this informative write up on the process of How_to_Ask_for_Help. Often in our frustration we overlook the obvious. How_to_Ask_for_Help serves as a nice guide on the steps to take in building a good help request (good for you and good for the person you're asking). It helps cut through the frustration and confusion in order to get to what we're really looking for. . . Answers!
After you've got a well formed support question, fire an email off to CCN Support. You'll receive updates on the status of your inquiry, notification by email when the issue is resolved, and links to possible solutions.