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Helpful Website for Intro to MRI Physics: https://www.mriquestions.com/index.html ''' '''
- The Office
LCN Orientation for New Staff
- Things to do during your first week
- Other things to know & do
- Lab Basics
- Learning the Basics
- MGH-related Living & Commuting
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
Welcome to the lab! You have likely already received many instructions from MGH HR and/or Martinos Center administrators (Carol & Alex). Please follow all of their directions and make sure to complete all the required training & appointments they mention.
Here you'll find more information than you need about our lab and getting started here. Please read through everything, however, below is a short list of the most important things to give your attention:
- Give your supervisor and/or Allison your MGH employee ID # (on the back of your ID card), the 6 digit # on the back of your ID in the top right corner, Partners username, your MGH email address, a photo of yourself and your birthday.
If you are sitting at a desktop machine in the lab, read the Your Computer section.
Complete IRB training (if it applies), wet lab training (if it applies), and Fire Safety training as soon as possible. See the Training section.
If you plan to use the MRI scanners, sign up for the mri-scan mailing list.
If you're using a laptop and connecting to the Partners network (via wired connection or non-guest Partners wifi), that laptop must be encrypted. Read more here.
Things to do during your first week
ID Card Access
When you first get your ID card you will not have access the building or any of the floors and labs. On Mondays and Thursdays, from 11am - 1pm, in the cafeteria, there is a booth for setting up security card access. The guard will ask who you work for and where you need access to - and in a few moments your card will be set up.
To get ID card access to the scanner bays, you must take the scanner safety course with Mary O'Hara. Once you've taken the course, Mary will submit your ID # to Donna for access.
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 email@example.com and tell them your nmr username, 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 fill out this Google Form. 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.
For more information, see LcnAdmin#Machinesinthelab which includes a link to our list of machines, their specs, and locations for storing data.
Your Desk Area
Welcome to your new desk! Please create and print a name tag for yourself using the desk label template located here:/autofs/space/andromeda_001/users/lcn/Desk_label_template_Apr2018.docx You can hand this printed name tag to Leah Morgan (2248 N) if you would like it laminated.
The following can be done once you have set up a wiki account and if you are comfortable with editing wiki pages:
Also take note of the name of your computer located at your desk. Go to the LCNComputers wiki page and edit the page so that your name is reflected as the new user. Email firstname.lastname@example.org to ask to receive email backup notifications(only required if you're a permanent employee) and once this is enabled, you can add your username to the relevant column.
There is also a desk layout image at the bottom of the LCNComputers wiki page. This is the jpeg image of a power point slide located here: /autofs/space/andromeda_001/users/lcn/LCN_lab_layout_for_LCNComputers_wiki.pptx. Edit the slide so that the layout reflects the correct computer name at your desk and so that your name is also reflected. Export the slide as a jpeg image (you can write over the LCN_lab_layout.jpg file that is there already). Then, click on attachments at the top of the LCNComputers wiki and upload the new jpeg file. If the name hasn't changed you shouldn't need to edit the text of the wiki page, but if you saved the file as a different name you will need to edit the text to point to the new jpeg attachment before it will appear at the bottom of the page. For help, contact Leah Morgan.
Martinos Center Account
In order to log into your computer in our lab, log in to the scanners, or get access to files on the network, you need a Martinos Center login. This is different from your Partners login which was assigned to you when your employee/nonemployee paperwork was approved (and was likely given to you during orientation or by Carol Barnstead). As of 2016, the same username will be used for Martinos Center as is used by Partners but the passwords will be different unless you opt to sync them (the Martinos Center helpdesk will email you information on how to do this).
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 'nmr' email address.
Check your Partners email here.
IRB notifications & Martinos Center password change requests will be sent to the Partners/MGH email account so it is important to check it regularly. For example, if you don't change your passwords when it is requested, your accounts will be closed.
You can use Thunderbird, Outlook, or any other mail program on and off-campus. You'll find *a lot* more information about setting up email in the Even More about Email section below.
But 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):
Martinos Center Mailing lists
You can see the list of possible mailing lists you sign up for here. Of those on this list, it is highly recommended to join brainmap, whynhow, and community in addition to any others that interest you.
If you will be involved with FreeSurfer development, it is suggested you subscribe to the freesurfer list as well as fsdev (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fsdev).
If you are an RA working for Bruce, please sign up for these mailing lists:
freesurfer, bay5scan, mri-scan, batch-users, small-bore, fsdev (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fsdev)
Update your Partners profile with your location and phone number by following the directions here. You can also sign up for the MGH and MGH Research email lists for important hospital-wide announcements.
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 (send an email request for a wiki username): https://surfer.nmr.mgh.harvard.edu/fswiki/GettingAccess
Once you have a username, you can create a wiki or edit an existing one.
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. Partners uses the CITI program for this training, so it's often referred to as your CITI certification (instead of IRB training).
There are three different courses to choose from, but EVERYONE should take the "Biomedical Research Investigators and Key Personnel BASIC Course".
Follow the below instructions to complete the training:
Go to https://www.citiprogram.org. Click the Register link at the top.
- Search for 'Massachusetts General Hospital' in the 'Select Your Organization Affiliation' box. You need to start spelling the full name and then some options will pop up that you can select. Agree to the terms of service and click 'Continue to Step 2'.
- Enter your first and last name and a primary and secondary email address. The primary email should be the address you will use to communicate with Partners or your hospital about IRB training. Click 'Continue to Step 3'.
- Enter your Partners user name (preferable). If you do not have one, you may create your own.
Create a password using 8 to 12 letters and numbers. This password should be different from your Partners password. Also select a security question and provide an answer, in case you forget your password in the future. Click 'Continue to Step 4'.
- Enter your country of residence. Click 'Continue to Step 5'.
- Check “No” for CME/CEU credits, answer the course survey question, and hit the 'Continue to Step 6' button.
- This will bring you to a screen requesting additional registration information your hospital may require. Insert the requested information and hit the 'Continue to Step 7' button.
- Select the boxes that apply to your research. If you don't know which apply, at a minimum select you will be working with humans. Click 'Next'.
- On the Education Requirement page, select biomedical research or "I have previously completed the Basic Course and need to take a Refresher Course" if this is the case.
- If no one has told you to take the Good Clinical Practice course, select Not Applicable.
- After this is submitted, you will be brought to the main menu. Select the Biomedical Resesarch Investigators and Key Personnel course.
- You are now ready to start the modules. Follow the directions for each module to complete. You may stop and start the course as you wish.
- To resume, login with your CITI username and password. If you have forgotten your login information, click the Forgot login Information button and it will be sent to you. Click the Re-enter link under My Courses.
When you have completed all of the fifteen (15) required modules for the Biomedical Research Basic Course or the required modules for the Biomedical Refresher Course successfully, you will be able to print a copy of your completion report. Please retain a copy of the certificate for your records. You may be asked to provide a copy to your hospital or sponsor.
Please email Allison (astevens AT nmr.mgh.harvard.edu) a copy of the completion certificate so she can add you to the appropriate IRB protocols.
You'll also need to send Allison a dated electronic copy of your CV (with the date added to the top) for the IRB records.
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 Wet Lab Personnel:
Please complete the course called "MGH General Safety Training" within 30 days of your start date. Training is here. You will be notified via Healthstream to renew this training each year.
For Wet Lab Personnel:
Please complete the following courses within 30 days of your start date. Note: You may or may not be prompted each year to renew these - you must remember to do so on your own:
"MGH Chemical Hazard Communication in Laboratories" - not required but preferred it is completed according to EH&S
**Please note that anyone who goes into the wet labs or scanner bays must wear 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, wear goggles and a lab coat.
Finally, take note of the nearest fire extinguishers, fire alarm pull stations, and emergency exits.
Other (Possibly Required) Training
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.
For the green badge exam, review the material found here and make sure you can do all the items on the green badge checklist (located on page 33-34 in the pdf). Once you feel ready, email email@example.com to set up a time for your green badge exam.
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 Joe Mandeville for access and training.
Wet Lab Training
Shipping Infectious Substances Training
If you will be working in the wet lab and shipping or receiving shipped tissue samples, you must complete the training below:
http://intranet.massgeneral.org/ehs/ehs_programs_trainingprogram.htm#2 Completed Bill of Lading forms (and all shipping documents) should be kept for 3 years. For more details see the ExvivoTransport page.
MGH Chemical Hazard Communication in Laboratories
This training is about the signs posted on chemicals, fridges, and lab doors. It's on healthstream under the above name. You can get to it after logging into healthstream via this link.
Active Shooter Training
MGH offers training on what to do in the event of a shooter on campus:
Other things to know & do
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.
Join the Lab Mailing List & Calendar
Ask the lab manager to subscribe you to the lab's email list once you have your MGH email, if you haven't yet received a subscription notice.
Subscribe to the lab google calendar to see upcoming lab meeting details and other events. Email the lab manager with the email you want to use to access it (gmail preferred).
Lab meetings are Wednesdays at 2pm in Chesler Library. Lab meeting agendas or cancellations are emailed out a day or two before the meeting.
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 Allison so she can update the page with your info. Be sure to send a photo as well!
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. If you are a Fischl RA, go here (under the Miscellaneous section) for Bruce's information to put on your application. It is good for one year and must be renewed each year by filling out the application form (selecting "Renewal" under Section 2) and mailing in or dropping off the $5 renewal fee. They accept Visa, Mastercard, cash and checks (made out to Coutnway Library).
Important Phone Numbers
- Security Desk- x6-5400
Environmental Health and Safety, Martinos office - x6-0191 (first contact for chemical spills, hazardous waste removal)
Environmental Health and Safety, MGH main campus office - x4-8419 (call for seriously hazardous chemical spills, report fire hazards, chemical exposure, etc. Do not call for waste removal)
- 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)
- MGH Operator- x6-2000
- Bruce - x6-4897
- Allison - x6-4050
- RA Desk Phone - x6-6598
- Biochem Lab - 643-3699 (our lab downstairs where we pack brains)
- Bay 5 - x4-8840
- RF Lab - 643-5106
- Parking - x4-6588
- Polycom phone # in Chesler - 617-724-8406
For information about wet-lab procedures, please refer to this page: https://surfer.nmr.mgh.harvard.edu/fswiki/WetLab
For MGH (non-Harvard) Employees
Please read through and add to this RA-created wiki which has frequently asked questions a Research Tech might ask:
You can view your payroll information in Peoplesoft.
Even if you sign up for direct deposit on Peoplesoft, your first paycheck may be in paper form. Pay day is on Thursday, but it is retroactive, so you will get your first week's check during your second work week. Sign in to Peoplesoft and go to the Self Service section (in HRMS Production). Click on the tab for payroll and compensation and then navigate to "view paycheck" to validate that you have a pay stub for your first week. At the bottom of the summary, you will either see "issue check" or "direct deposit." If you see "issue check," your first check will be in paper form. Go to the HR office on the 7th floor to claim your check. If you do not pick up your check within the first 2 weeks of employment, it will be mailed to your address on Peoplesoft.
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.
Alex Hogue is your timekeeper. As of April 2016, there is a new email address ( firstname.lastname@example.org ) where you should send your time off information. Please cc Allison on all emails sent to timekeeper@nmr.... Allison will give you a copy of the lab's earned time policies.
Below is the Martinos Center Timekeeping Policy (from April 2016):
This Policy applies to all weekly paid employees both exempt and non-exempt.
All use of EARNED TIME needs to be approved, in advance, by your supervisor/manager.
As part of our effort to make timekeeping simple for the center, we are pleased to announce the new email@example.com email. The purpose of this new email address is to inform the person who is timekeeper as to when you are taking time off. Please follow these simple steps.
1. If you currently are submitting Kronos e-forms for corrections, please continue to submit these corrections.
2. If you submit your hours electronically please send these emails to the new centralized email mentioned above.
3. Please make certain that you obtain prior approval from your immediate Supervisor/Manager for requested time off, such as vacation, personal days etc. Once approved please forward the timekeeper with a copy to your supervisor/manager of your dates at the above email address.
4. Please also notify the timekeeper of non-scheduled days off such as sick days, etc. so he may make the necessary notation in KRONOS.
This new email will obviously take some time to get accustomed to but after a while it will help us keep better track of requests. Lastly please do not hesitate to contact the timekeeper, Alex Hogue or Donna Crowe if you have any further questions.
Please find below the link to the Partners Health Care Policy Manual referring to Attendance and Punctuality.
If you are having trouble with your Partners or MGH emails or accounts, contact the Partners helpdesk: http://helpdeskselfservice.partners.org/
Martinos Center Helpdesk
If you are having trouble with your Martinos Center account, cluster access, launchpad access, see the Computer Resources section of the LcnAdmin wiki for information on what to do. Remember to always include your nmr username and the name of the computer giving you trouble, otherwise Help will just reply asking for this information which will slow things down!
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'.
If you need to scan a document (not a brain!), you can use the copier machine located across from Janice White's desk in the administrative area, or the scanner in South Central attached to the Partners PC.
Data Access 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
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. More information about encryption is provided on the LcnAdmin wiki.
Note: You cannot forward your Partners or Martinos Center email to another email address (i.e. gmail, yahoo, etc.).
Even More about Email
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 may 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. It will take about two days to process, and you will get an email to confirm the change.
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, you must be faculty.
Tip #1: 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!
Tip #2: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 @pdc" followed by the person's name or username, and hit enter.
Example: finger @pdc janedoe
Changing your email address on mailing lists:
If users are subscribed to mailing lists with their @partners.org address, and then later they have their default address changed to @mgh, they will need to unsubscribe the old address and subscribe the new address in order to be able to post messages to the list. This can be done for all mailing list with one step by clicking on the link to unsubscribe or change your options in the confirmation email from any Martinos Center mailing list. Sign in with your password and then enter the new address in the 'Changing your [GroupName] membership information'. Checking the box that says 'Change globally' will do this for all of your mailing lists.
Setting up Pine
Many of our lab members use pine (type 'pine' in a terminal to use it), however, this only works with the old nmr.mgh.harvard.edu email addresses. Sam Mehl is working on making pine work with Partners emails. See this page for what needs to be done (as of 8/31. General info on setting up email is here:
**When using pine, the ^ symbol refers to the Ctrl key.
Setting up Thunderbird
In order to set up Thunderbird using Exchange, you need to download the ExQuilla addon. (NOTE: This is an older method. You might prefer to use IMAP so you don't have to pay for Exquilla.) 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 @partners.org email address and password, and choose the Login with username and domain option. For username, put in 'partners\YourPartnersLogin', then press next. Click the 'do auto discover' button, click next again, and then click finish. This will allow you to access Partners emails from Thunderbird. The From box of your new emails will show your @partners.org address, but it will send as @mgh.harvard.edu if you chose that as your default address. However, after a period of time the Exquilla addon will you require to pay money in order to continue using it.
You can also access your Partners email (<username>@partners.org or <username>@mgh.harvard.edu) on Thunderbird without using Exchange. Here are the configurations:
Email address: <FLastname>@mgh.harvard.edu
Username: Partners ID
Incoming server: imapx.partners.org
Connection security: SSL/TLS
Authentication Method: NTLM
Outgoing server: smtpx.partners.org
Connection security: STARTTLS
Authentication Method: Normal Password
Unfortunately, accessing emails that have been moved to the Enterprise Vault (emails >90 days old) must be done using a web browser. Thunderbird is a "compatible email client", so archived emails will show up in a truncated form in your inbox. Only the part of the message that is in the truncated version can be searched. After clicking on the message, you will be given a link to access the full message. To access the Vault directly, go to https://archive.partners.org/EnterpriseVault/. More information from Partners on accessing the Vault using Thunderbird can be found here
For "gmail-like" conversation views of email (where replies are grouped together with the main message, instead of being separate messages in your inbox), install the Thunderbird Conversations add-on. Go to the Thunderbird menu, click on Add-ons, and it should be on the front page (if not search for it). Follow the instructions to install.
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/
Helpful Website for Intro to MRI Physics: https://www.mriquestions.com/index.html
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.
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.
Why & How Schedule
A lecture series that teaches the basics of a wide variety of topics:
MGH-related Living & Commuting
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
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.
Savin Hill area has some nice temporary housing. Contact Mary Lynch at email@example.com
Don't know anyone who has used this site but Louis came across it:
MGH Commuter Services Their website 617-724-6588
- Charlestown Navy Yard Parking Garage (Building 199) - prices as of 10/2/16
monthly pass- unlimited 24/7 access- $120 (taken out of your paycheck after tax weekly)
- or can buy 20 debits (single entry/exit per debit) for $140 - no expiration date
Discount T pass
For rates, see this website.
You can sign up for a discounted T pass through your Peoplesoft account. After signing in, click on HRMS production, Self Service, Payroll and Compensation, then MBTA Pass Enrollment. You must sign up on or before the second Thursday of the month PRIOR to use (ex. sign up June 10th for a July pass). Carol should have your pass a few days before the 1st of the month. If you sign up after the 2nd Thursday of the month, or Carol does not have your pass, you must get it from the Commuter Services office on the main campus (232 Wang).
Paychecks are deducted on the third paycheck of the month.
If you initially get a discounted T pass from MGH, but later decide that you want to drive to work everyday and park in the CNY199 Parking Garage, you will have to give up your discounted pass. (You cannot sign up for monthly parking at the parking office in the garage until you have canceled your T pass in PeopleSoft.) MGH subsidizes the T pass on the basis that that is how you get to work everyday. If you sign up for monthly parking at the garage, they know you are no longer using the T to get to work, so you cannot keep the discounted pass. Unfortunately you cannot just add money at a T ticket kiosk to your existing CharlieCard that you got from MGH. The MGH Parking and Commuter Services office said this is because our cards are special corporate cards that are encrypted, so you can't add your own money to it. Allison M. went to the MBTA ticket office at North Station in March 2015 and they confirmed this. You must simply get a new CharlieCard. (You do not have to give them your old MGH card, and Carol didn't say that we had to hand them back into her either.)
Benefits for Non-drivers
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
As of the end of October, 2014, there is a bicycle cage with ID access inside the garage across from Building 149. You must go to the garage office (hours: Mon-Fri, 8AM-4PM) and fill out a form with your bike make, model and serial number to get a decal for your bike and to get access to the cage. There is a one time $10 fee. Unless you have a decal, MGH security has the right to remove your bike without notice. The bicycle racks in front of the building are supposed to be reserved for visitors.