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==== Setting up Thunderbird
In order to set up Thunderbird, you need to download the ExQuilla addon. Information on how to do this can be found [[http://www.techrepublic.com/blog/smb-technologist/connect-the-thunderbird-email-client-to-your-exchange-server/|here]]. Basically, go [[https://exquilla.zendesk.com/home|here]] and download the current release for Linux. Open Thunderbird, go the Addons menu, then click on the tools button (next to search bar) and Install addon from file. You'll need to restart Thunderbird.
To get access to your email account, some useful information can be found [[http://rc.partners.org/kbase?cat_id=1&art_id=198|here]] and [[http://www.techrepublic.com/blog/smb-technologist/connect-the-thunderbird-email-client-to-your-exchange-server/|here]]. Go to Tools -> ExQuilla for Microsoft Exchange and then select Add Microsoft Exchange Account. Type in your email address and password, and choose the Login with username and domain option. For username, put in 'partners\<Your partners login>', and for domain put in 'outlook.partners.org'. This should allow access to Partners email from Thunderbird.
- The Office
LCN Orientation for New Staff
Things to do during your first week
- ID Card Access
- Martinos Center Account
- Your Computer
- Create a Wiki Account
- Get a Harvard ID
- Lab Notebook
- Once you have Partners and Martinos Center accounts
- Research Assistants
- Things to do during your first week
- Lab Basics
- Martinos Center Basics
- Partners/MGH Basics
- Learning the Basics
- Life Basics
Important Phone Numbers
- Security Desk x6-5400
- Fire/Chemical Safety- x4-8419 (chemical spill, report fire hazards, chemical exposure, etc.)
- Buildings and Grounds - x6-5270 (fix broken fixtures, change light bulbs, move furniture, install whiteboards etc.)
You can submit work orders online here. It requires your Partners password. Building issues such as loud vents or temperature issues do not require a fund number.
- Environmental Services - x6-5490 or email CRIVERA3 at PARTNERS dot ORG (book conference rooms, housekeeping issues)
You can see conference room availability through your Partners email. Click on Public Folders (bottom left once you're logged in). From there, click on the arrows that precede the following words: Partners > MGH > Research Affairs > Conference Room. You cannot book a room through the website, you can only see availability.
- MGH Operator x6-2000
- Bruce - x6-4897
- Allison - x6-4050
- Biochem Lab x-65823 (our lab downstairs where we pack brains)
- Bay 5 x4-8840
- RF Lab 643-5106
- Parking - x4-6588
Our room # is 2248 but the Admin office where mail goes is 2301. Our full address is:
Massachusetts General Hospital
Athinoula A. Martinos Center for Biomedical Imaging
Bldg. 149, 13th Street, CNY 2301
Charlestown, MA 02129
Directions to our location
You can find directions to our location here:
LCN Orientation for New Staff
Things to do during your first week
ID Card Access
When you first get your MGH ID card, it probably will not let you into doors on the 2nd floor. Allison or your supervisor can request door access from Dee Dee (who will then send the request on to security). To do this, Dee Dee needs your employee ID # (located on the back of the card above the barcode) *and* the 5 or 6 digit number printed sideways on the back of your card (there might be another long string of numbers that comes after it - you can ignore those).
It can take a few days to a week before your card starts working. This is frustrating! But please be patient and keep testing your card to see if it has been activated yet. If it still isn't working after a few days, check with Dee Dee to make the request went through. Note: It is not necessary to take the MR Safety course before getting access to the 2nd floor. This has been confirmed with Dee Dee as of February 2014.
Martinos Center Account
In order to log into your computer in our lab or get access to files on the network, you need a Martinos Center login. This is different from your Partners username which was assigned to you when your employee/nonemployee paperwork was approved (and was likely given to you during orientation or by Carol Barnstead).
Allison or another supervisor can request an account for you on this website. To do so, they will need your current email address, your Partners username (it will contain your initials and a number, i.e. AAS41), your MGH ID #, and a picture of you. Note that you are not allowed to forward Partners or Martinos Center emails to gmail, yahoo, or hotmail addresses.
Your Martinos Center account can take up to 48 hours to be created. In the meantime, Allison or Lilla can set you up on a guest account for you to work on a computer in the lab while you wait. Once your Martinos Center account is created, you will have an nmr.mgh.harvard.edu email alias that fowards to your Partners email account. However, you won't be able to send emails from this 'harvard' email address. If you would like a 'harvard' email address, follow the instructions under the Email section for creating an mgh.harvard.edu alias.
IRB notifications & Martinos Center password change requests will be sent these email accounts so it is important to check them regularly. If you don't change your passwords when it is requested, your accounts will be closed. You can check your Partners email here.
Feel free to use Thunderbird, Outlook, or any other mail program on and off-campus. The majority of the lab uses pine (type 'pine' in a terminal to use it). Info on setting up email is here:
**When using pine, the ^ symbol refers to the Ctrl key.
And be sure to follow the Encryption rules (to summarize: you can't access email without an encrypted laptop; non-public desktops are okay; phones have additional requirements):
Set up your Partners profile so you can be added to the Partners database here. On that website, chose MGH for the email distribution list to get important hospital-wide announcements.
==== Setting up Thunderbird In order to set up Thunderbird, you need to download the ExQuilla addon. Information on how to do this can be found here. Basically, go here and download the current release for Linux. Open Thunderbird, go the Addons menu, then click on the tools button (next to search bar) and Install addon from file. You'll need to restart Thunderbird.
To get access to your email account, some useful information can be found here and here. Go to Tools -> ExQuilla for Microsoft Exchange and then select Add Microsoft Exchange Account. Type in your email address and password, and choose the Login with username and domain option. For username, put in 'partners\<Your partners login>', and for domain put in 'outlook.partners.org'. This should allow access to Partners email from Thunderbird.
MGH/Harvard Email Addresses
Most full-time employees will automatically have their @partners.org email linked with their @mgh.harvard.edu address (if you send an email to yourself, does it come from @partners.org or @mgh.harvard.edu?). Bulfinch Temps & nonemployees will not be given an @mgh.harvard.edu address.
However, if you only have an @partners.org email address and you would prefer to have an @mgh.harvard.edu address (note the lack of 'nmr'), send an email to EmailAccess@partners.org from your Partners account and ask that your primary email address be changed from @partners.org to @mgh.harvard.edu.
When you email this request, specify which of the two formats you would like to use for the email. If your address is, for example, firstname.lastname@example.org you can request email@example.com or you can also request firstname.last name, eg firstname.lastname@example.org
After your default address is changed, mail sent to the original @partners.org address *will* continue to reach you. All outgoing emails will have the new harvard.edu suffix.
If you want to be able to send emails using the full @nmr.mgh.harvard.edu, get published, get grants, join our faculty, and you can have one.
Tip: Typing out "@nmr.mgh.harvard.edu" or "@mgh.harvard.edu" can get annoying! You can substitute the "@nmr.mgh.harvard.edu" or "@mgh.harvard.edu" with "@martinos.org" and it will still work!
If you would like to look up the email or username of a Martinos Center employee, you can use the "finger" command in a terminal window. Type in "finger," followed by the person's name or username, and hit enter.
Example: finger janedoe
Important: MGH Privacy rules dictate that you must lock your computer screen whenever you walk away from your computer. Please be diligent in doing this.
In this lab, we usually have several users to each machine. Thus, this might mean others are physically sharing the same desk as you, others are storing data on the machine you are using, or others are ssh'ing to the machine you are using and running processes on it.
This means one very important thing. DO NOT turn off your machine.
Here are a few other important notes about the computer you are working on:
- If there is a problem with your machine that cannot be resolved by you or fellow lab members, email help AT martinos dot org and tell them the machine you are using (every machine is labeled with a name) and what went wrong, being as specific as possible.
- If your machine seems to be slow, run 'top' in a terminal window to see if other users might be running intensive processes on it. Contact that user to let them know it is slowing down your work. Feel free to contact the lab manager at any point to get help finding another machine where these processes can be run.
- If you need a space to store data, please contact your supervisor and/or the lab manager to request space. If you save data on your machine, it *might* be deleted after you leave or when the machine dies. If you save large amounts of data in your home directory, you will go over quota quickly. In order to check your quota assignment and your current usage type "quota" in your terminal window and it will display all the details.
- If you need to run intensive processes on a machine (because the cluster is not an option), check with the lab manager on which machine is most appropriate.
- If, for some reason, your machine needs to be rebooted or turned off, follow these directions:
- Run 'top' in a terminal window to see if anyone is actively running any processes on it
- Run 'last' and 'w' to see who generally accesses that machine and the most recent dates they needed it
- Check the local disk space at /space/machinename/*/users to see who saves files there
- Email the above users to make sure it will not interrupt their work if you shut down the machine. When in doubt, email the lcn mailing list.
Create a Wiki Account
We use a wiki to not only document FreeSurfer, but to document our projects as well. You will probably be asked to create a wiki in order to document your work. In order to do this you will have to get a wiki username. You can do that here: https://surfer.nmr.mgh.harvard.edu/fswiki/GettingAccess
Once you have a username, you can create a wiki or edit an existing one.
Get a Harvard ID
If you are a research fellow, you may have a courtesy/affiliated appointment at Harvard Medical School (nonemployees & visiting fellows do not). This grants you access to Harvard libraries & full text articles online; free admission to Harvard museums; and use of Harvard athletic facilities for a fee.
To get your Harvard ID, go to the Harvard ID office at 1350 Massachusetts Avenue in Cambridge (By train, take the red line to Harvard Square. The office is located in the Holyoke Building on the corner of Massachusetts Ave & Holyoke Street near the Au Bon Pain restaurant). You will need to show your MGH ID and a passport or license (if you are a U.S. citizen) to prove your identity. The office is open from 9-4:45, Monday through Friday and can be contacted at 617-495-3322.
If you are a research assistant, you can get a Harvard ID by following these instructions. This will only give you access to the library and online journal articles.
You can get a lab notebook by going to see Carol Barnstead. She will sign one out for you. This lab notebook will have to remain at MGH if you leave your position here.
While you wait for door access and account access, be sure to take care of the required training described below. Aside from that, you can also read up on how things work in the Lab, the Martinos Center, MGH, and so on.
You are required to meet a variety of training requirements depending on what type of work you will do here. Just about everyone must do the IRB Training & the Fire safety training.
You will have to renew this training every 3 years.
In order to work with human subjects data, you must be certified to do so. To get certified, you have to read a couple of articles and then take a quiz on the material you have read. This takes a few hours but is important to do before you can start work on any projects. You can find information on how to do the training here:
When you have successfully completed the course, please email Allison (astevens AT nmr.mgh.harvard.edu) a copy of the completion certificate (you may want to keep a copy for your own records) so she can add you to the appropriate IRB protocols.
You'll also need to give Allison a print out of your CV with your signature and the date at the top.
Fire Safety Training
This training must be done once a year.
If you've never logged into healthstream before, it takes your Partners username and the password abc123.
For Non-Lab Personnel:
Please complete the course on Fire and Safety training for Research & Clinical Lab Personnel within 30 days of your start date. Training is here.
For Lab Personnel:
Please complete the course on Fire and Safety training within 30 days of your start date. Training is here.
**Please note that anyone who goes into the wet labs or scanner bays must where closed-toe shoes. Those who enter one of our wet labs should be mindful of wearing gloves when touching anything in there & be sure to wash your hands after you are done. When appropriate, where goggles and a lab coat.
Finally, take note of the nearest fire extinguishers, fire alarm pull stations, and emergency exits.
MR Safety Training
If you plan to spend any time in the scanner bays, you will have to do the MR Safety training.
For the large bore scanners, subscribe to the mri-scan email list to get announcements about the next scheduled safety training. Mary Foley (O'Hara) holds a safety course about once a month and sends the dates and times for this course to this list. The training consists of watching a video and taking a quiz. If you pass the quiz, you will get a yellow badge which allows you in the scanner bays with supervision. Four months after you receive your yellow badge, you can take the exam to get your green badge which allows you to scan without supervision.
Once you complete the MR safety training, ask Allison to request a scanner login account for you from Karen Dervin (you may already have one if Allison requested it when you were first hired) & to add you to the appropriate scanner projects.
For small bore scanners, contact George Dai for access and training. You will have to attend scan sessions with an approved supervisor until you feel comfortable to take the small bore scanning exam.
Shipping Infectious Substances Training
If you will be working in the wet lab and shipping tissue samples, you must complete the training below:
Active Shooter Training
MGH offers training on what to do in the event of a shooter on campus:
Once you have Partners and Martinos Center accounts
Encrypt & Register Your Laptop
You must encrypt your laptop, iPad, iPhone, and USB drives which access the Partners network/email and/or store patient health information or other private information. If you're checking your Martinos Center email from a device that isn't encrypted, you are violating this policy. Info on encryption is below:
In some cases, lab members are provided with laptops. Before you encrypt your personal laptop, check with your supervisor to find out if you will be provided with one.
Note: You cannot forward your Partners or Martinos Center email to another email address (i.e. gmail, yahoo, etc.).
Join the Lab Mailing List
Ask Allison to subscribe you to the lab's email list once you have your MGH email if she hasn't already.
Update Martinos Center Profile
Set up your Martinos Center profile to be displayed on the martinos.org website. Directions for how to do so are here.
The lab has its own website where your profile can also be displayed:
Please send a brief description of your background and what you're working on to Louis (vinke@nmr) so he can update the page with your info.
If you are a nonexempt employee, you will have to clock in every day at one of the Kronos Timekeeping systems. Information about these systems can be found here:
Please read all the information on the page and on the links at the bottom of the page.
Kaley (kaley@nmr..) is your timekeeper. Please cc Allison on all emails sent to Kaley. Allison will give you a copy of the lab's earned time policies.
Please read through and add to this RA-created wiki which has frequently asked questions a Research Tech might ask:
You can find many more details about the lab, Martinos Center, and MGH at the LcnAdmin wiki. You'll need a wiki username and permission to view it if you haven't already been granted permission.
We have lab meetings every Wednesday at 2pm in Chesler Library (and occasionally in room 2695).
Emails about what will be covered during the meeting go out each week to the lab email list (lcn@nmr...) to which you can also send announcements once you have been added to the list (Allison or Lilla can add you).
Group & IRB Permissions
A list of the lab's unix groups and IRBs are on the page below. If you need to be added to a group to gain file access on the network, let Allison know - she and Bruce are the only people who can request access. You will have to be on the appropriate IRB before you can be added to the corresponding group: https://surfer.nmr.mgh.harvard.edu/fswiki/LcnAdmin
If you need to print, you can send jobs to 'decacolor' which is located in the same area as the fridge. To print double-sided, print to 'decadouble'.
LCN online notebook
You can find some helpful tips from the life-practical (the process of getting a bank account for someone who just moved to the U.S.) to work-helpful (common commands used in exvivo processing): www.evernote.com username: lcn149 password: ask Allison, Louis, or Maritza
Documentation for FreeSurfer is on the wiki:
You can find online tutorials teaching you how to use FreeSurfer here:
Before downloading the tutorial dataset, check with Allison to see if she has a copy already downloaded that you can use.
There are two versions of FreeSurfer you will likely use while here. There is the developmental version - this is the most up-to-date version of FreeSurfer with all the latest features & all the latest bugs (!). And there is the stable version - this is the version that has been tested & is less likely to have bugs or problems. If you are running a subject through the FreeSurfer processing stream (recon-all), most likely you want to use stable. If you are simply looking at data, perhaps you'll want to use dev so you can use the most up-to-date version of freeview, our image GUI. It's always a good idea to ask your supervisor which version to use for each task.
To source the dev version, open a terminal and type:
To source the stable version, ask which FreeSurfer version is the latest. As of June 2014, that is:
The developer's guide with information about checking out code, adding new binaries, etc. can be found here
If you want to search for something on the wiki, you'll have the best luck if you click the 'Text' button to search rather than the 'Titles' button. You can find a full list of all material on the wiki here:
To learn more about FreeSurfer, you can sit in on one of our local FreeSurfer courses or lectures. Check with Allison to see when the next one will be.
Martinos Center Basics
Topics include remote access, purchasing cluster storage space, purchasing hardware & software, mailing lists, web space, etc.
To get access to the computational clusters, specifically launchpad, email kaiser AT martinos dot org and cc Allison when you ask for a launchpad account. Information on how the clusters work can be found in the two links below.
Also see the lab's evernote account for information on how to submit jobs to launchpad.
All papers published while working at the Martinos Center must acknowledge the P41 grant which pays for a lot of the resources at the Center. You can acknowledge it as "NIH (National Center for Research Resources) P41-EB015896". For MGH logos and a list of grants to acknowledge based on resources/systems you use, you can find that here: http://www.nmr.mgh.harvard.edu/martinos/userInfo/operations/miscOps.php
All manuscripts using ADNI data must be reviewed and approved by the ADNI Data and Publications Committee prior to submission. The DPC will strive to have a response back to you within 10 working days after you submit your manuscript so as not to slow down your efforts. Any manuscript submissions or questions may be submitted to email@example.com
Let Louis know (vinke AT nmr...) of any new publications or exciting news so he can post it on the lab website.
*****ATTENTION!!!: If you have a strict page number limit like in a workshop publication, consider if you want to use ADNI data in the first place or leave at least one page free for the ADNI acknowledgements and author names.
Don't wait until last minute or there will be a long queue!
Why & How Schedule
A lecture series that teaches the basics of a wide variety of topics:
MRI Scanner Info
(where we can sign up for time on the scanner):
Time Slot Rules
- Any slot that is listed as 'OPEN' can be grabbed. If there is a time you would like for which no slot exists (for example, 6-7am), email mri-time to request the slot and they will add it to the schedule. (For bay 5, you can add these slots yourself with the 'Add' button.)
- For all slots you take and are assigned, you must enter the names of the individuals who will be doing the scanning during that slot. To do this, click on the slot and then click "Edit Note". If you do not have names in the "Note" section then Mary or Larry can give the slot to someone else.
You can sign up to be notified when slots are released. Most often these are slots in the immediate future but you'll also see slots that are released far in advance: https://www.nmr.mgh.harvard.edu/facility/secure/schedule/notify.html Under Bay 4, for example, you would select "Open" to receive these notifications.
- Slots must be cancelled 24 hours in advance or you will be charged for the slot. A slot may be cancelled in less than 24 hours without being charged if you have a valid excuse like "last minute subject cancellation", "subject illness", "subject no-show", "subject discomfort".
- -Cancellations that are less than 24 hours in advanced must be emailed to mri-scan so others are alerted to the open slot. If you have a valid excuse, you'll want to cc mri-time so you don't get charged.
If you are done with your slot early you must release the slot by emailing firstname.lastname@example.org and email@example.com this allows other groups to use the slot if they need to. You would make the subject line say something like "Bay 4 free until 11am today" and then in the email you would write "due to early finish" or any other reason that you are finished early.
Partners website to view your paycheck, sign up for health benefits and discount MBTA passes as well as anything else HR-related: https://peoplesoftportal.partners.org/login/login.asp?CTAuthMode=BASIC
Partners Telephone/Email Directory
(Below, you can sign up for Perks emails to learn about discount programs, etc.): http://pulse.partners.org/common/index.asp
MGH Commuter Services Their website 617-724-6588
- Charles Navy Yard Parking Garage (Building 199)
- $98 monthly ($22.62 taken out of your paycheck after tax weekly)
- Can buy 20 debits to enter the garage for $115
- Discount T pass - see their website above for rates
Guaranteed Ride Home: If you take the bus, subway, commuter rail, carpool, vanpool, bike or walk to work, you can receive a free ride home in the event of an emergency or unscheduled overtime. Now you can ease your fears of being stuck at work because of something that may happen once or twice a year. MGH Parking and Commuter Services pays all transportation costs, including tolls and gratuity the program is completely free for you! Register now to get your voucher number for PlanetTran, the Nation's first environmentally friendly livery service. Visit ABCTMA.COM to learn more.
Ridematching: Ever wonder if you may have a neighbor or co-worker whom you could share a ride into work with once or twice a week? You can use our on-line ridematching system to find out if others who live and work near you are interested in sharing a ride in a carpool or vanpool.
Cycling and Walking Rewards: Our “Workout to Work” program provides employees who bike or walk to work. Each month when you submit your miles, biked or walked, to a transportation organization called A Better City Transportation Management Association (ABC TMA), you will be rewarded with free safety equipment and chances to win other prizes.
Vanpool Subsidy: You can receive $220 over six months from the ABC TMA for joining a vanpool. A vanpool of 9-15 riders is the most affordable way to commute to work from New Hampshire, Central/Western Massachusetts and Cape Cod.
Carpool Subsidy: You can receive $210 over six-months when you join an existing carpool or form a new carpool. By covering up to $35 in fuel for six months this program helps reduce your costs of commuting to work.
Express Yourself: If you drive alone you can receive up to $100 per month for three months to purchase an MBTA Express Bus, Private Bus, or MBTA Commuter Boat pass. This can cut the monthly cost of your commute by almost 50%.
REGISTER IN THESE FREE PROGRAMS ONLINE AT www.abctma.com
Learning the Basics
Dictionary of terms: http://www.mr-tip.com/serv1.php?type=db1&dbs=Pulse%20Sequence
Intro to MRI: http://www.mritutor.org/mritutor/
Info on Coil Tuning: http://www.cis.rit.edu/htbooks/mri/chap-9/detail/det-d-1.htm
Martinos Center documentation for Siemens scanners: http://www.nmr.mgh.harvard.edu/~benner/siemens/N4/index.shtml
Martinos Center Scanner Usage: http://www.nmr.mgh.harvard.edu/~benner/siemens/N4/scanner/index.shtml
Bay 5 Helium webcam and coldhead reading: https://www.nmr.mgh.harvard.edu/~coldhead/
Bay 5 Helium boiloff plots: http://www.nmr.mgh.harvard.edu/~equipmon/coldhead/last2weeks.log_BoilOff.png
Unix & Scripting Tutorials
If you are unfamiliar with the UNIX operating system, there are many online tutorials. Here are a few:
Let Allison know if you are new to UNIX and she'll give you a few more resources.
Choosing/Being a Mentor
Slides from an HMS talk on this topic can be found here.
Most require a minimum 30 day stay and provide furnished housing.
National Corporate Housing
The West End Apartments
(Formerly Equity Corp. Housing)
5 Longfellow Pl, Ste. 102 Boston MA
Adjacent to MGH campus
221 Mass. Avenue, Boston, MA
Oakwood Temporary Housing
1 India Street, 2nd floor, Boston, MA
Ask for Maryellen Daly or Deidre Fistori
Interim Housing Solutions
National program matches individuals with furnished, short-term apartment rental.