Administrative

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Various administrative topics related to lab membership and experimental restrictions.

Contents

[edit] New Lab Members

[edit] Lab To-Do List

  • Before accessing or acquiring human subject data you must complete the on-line CITI (Collaborative IRB Training Initiative) course at the CITI website. If you completed this course at another institution in the last two years you can log on to your CITI account and change your affiliation to Stanford. We recommend that you print your certificate of completion for your records in case you are asked to produce it during an audit. Please note that for the Question 1 on the CITI ("Select Curriculum") you will need to select Group 1.
  • You will not be allowed in the scanner room until you complete safety training at the CNI. Please contact Laima Baltusis to arrange training.
  • Open an account on white (ask [mailto:lmperry@stanford.edu Michael Perry for help).
  • Obtain keys to the Wandell Lab and the front door of Jordan Hall from Facilities Manager Harry Bahlman, room 027 (723-2406). Harry's office hours are: Mondays & Wednesdays 12:30 - 2:00, Thursdays 10:00-11:30. There is a mandatory deposit of $10 per key; this will be returned in full when you leave.
  • Apply for a SUNet ID
  • Further questions? See Anh Le _, 3nd floor

[edit] Useful Resources

[edit] Psychology Department Administration Contacts

Stanford Psychology Homepage

[edit] Campus

[edit] Neighborhood

[edit] Holiday Events

July 4th Events

[edit] IRB approval

[edit] MEDICAL & NON-MEDICAL HUMAN SUBJECT PROTOCOLS & CONSENTS

All government and non-government sponsors require Institutional Review Board (IRB) human subjects approval (using a PROTOCOL & CONSENT forms) during the grant/contract performance period. It is a violation of University policy and federal regulations to recruit, enter, or follow subjects or analyze human subjects data without IRB approval. Proof of continuing approval must also be obtained throughout the funding period (RENEWALS).

The Medical Research web site below will provide you with all the information and forms needed to submit a NEW MEDICAL ePROTOCOL (regular, expedited, or exempt) or a NON-MEDICAL ePROTOCOL. Examples of consent forms and required language to be included in protocols and consents are also available as well as links to other important requirements. To apply for NEW MEDICAL human subjects approval, submit a Protocol and Consent form through the web site using eProtocol Submission under “Research." For NON-MEDICAL applications for approval use the Non-Medical forms and consent located under the same category.

Medical Research Web Site

Protocols are first reviewed by the IRB staff and then the IRB members, who will then make the final decision as to review type. IRB comments and questions are distributed to the investigator to be addressed prior to a convened meeting. All Regular protocols must be presented, discussed and voted on at a convened meeting of the IRB. This process generally takes approximately 4-6 weeks; click below for a schedule of submission deadlines and meeting dates.

IRB Deadlines and Meeting Dates

[edit] NIHMS - Uploading accepted manuscripts

Several publishers (see below) submit automatically.

If you need to submit, and you have the papers (PDF) and figures (PPT) and grant information, you can start the upload process from the NIHMS web-page. You must have an ERA Commons password and be prepared to list the grant(s) and co-authors who supported the research. So, either get me to do the upload, or ask me (or Pam) for the password.

[edit] Summary of methods

Concerning the submission to Pub Med Central (PMC), here are comments from our program officer, (May 8, 2010)

  • Only peer-reviewed papers are required to be submitted. Invited reviews, editorials etc are exempt.
  • There are 4 methods (A-D) for submission http://publicaccess.nih.gov/submit_process.htm.
  • Always check with the journal when you submit the final manuscript for publication.
    • More and more journals are submitting directly to PMC (Method A).
    • Some journals will submit directly to PMC but only if you ask (Method B).
    • If the journal doesn’t submit, you must submit to PMC using the NIHMS submission system (Method C).
    • A few journals submit for you, but use the NIHMS system instead of going directly to PMC. That requires some input from you (Method D).
    • For the first three months after publication you may use the [PMCID in progress] designation at the end of your reference citation.
    • Methods C and D will issue you a temporary NIHMSID number that you can use until the PMCID is issued.
    • After three months you go to PMC and get the PMCID number to include at the end of the citation http://publicaccess.nih.gov/citation_methods.htm#difference.
  • Most PIs are confused and use the PMID (the citation only in PubMed) instead of the required PMCID (full text in PubMedCentral).
  • Don’t worry about the duplicate submissions; PMC will figure that out.
  • “Open-Access” or “On-line” is irrelevant. All manuscripts must go to PMC.

There is a video describing the process at this location. There is a basic web-page describing the whole situation at the NIH as well, but I found it confusing. I believe that we use Method C.

[edit] Online resources

There is a list of journals and of publishers that automate the task or will do it if asked. I didn't see any familiar names when I last checked that list.

To see the papers with Wandell in the title that have been uploaded, go to PubMed Central, set the pull down for search to PMC, and search using

author manuscript[filter] wandell

or other terms. (Some of our papers do not include Wandell as an author).

[edit] Some Journal Policies

The vendor for IOVS, Cadmus, is depositing on behalf of authors  since the beginning of this year. 
No arrangements have been made for JoV as yet, but we hope to be able to provide this service  
some time in the near future.


[edit] Lucas Center

[edit] New User Training

To scan at the Lucas Center, you need to take an MR safety course. To sign up for the course go to Anne Sawyer's website and click on the New Users Page. You will be directed to fill out the account request form. Be aware that it could be up to three weeks before the course and you will not be allowed in the magnet suite until you have completed the course.

  • Group IDs: When filling out the training registration form you will be asked for group IDs in a comma separated list. That list should look like this:
 wand1f, wand2f

[edit] Scheduling Time

To schedule time on a scanner the Lucas Center, use the RSL users site. If you don't yet have a Lucas Center user account, you can request one by clicking the "Request a Lucas Center user account" link at the bottom of the RSL users site.

The protocols we use at the 1.5T and 3T are described in separate pages.

[edit] Lists

Stanford uses mailman, which has a nice web interface, for subscribing and managing lists. Visit the Stanford mailman start page to learn more.

Click on the links below to join the typical lab lists

In general, to join a mailman list, use:

 http://mailman.stanford.edu/mailman/listinfo/{list-name-here} .

[edit] VISTA Lab Group

Click on the links below to subscribe to the usual Wandell lab mailing lists

[edit] Psych

To be added to a list, email the list manager.

  • us-at-psych.stanford.edu (everyone) ~~ Manager: Bhavna Raval, braval@stanford.edu
  • psych-all-fac-at-lists.stanford.edu ~~ Manager: Pam Widrin, pwidrin@stanford.edu
  • post docs-at-psych.stanford.edu ~~ Manager: Beth McKeown, bmckeown@stanford.edu
  • students-at-psych.stanford.edu ~~ Manager: Beth McKeown, bmckeown@stanford.edu
  • cognitive-at-psych.stanford.edu ~~ Manager: Don't know
  • neuro-at-psych.stanford.edu ~~ Manager: Don't know

[edit] Stanford

[edit] Neurology

See the Stanford lists page to sign up.

  • neurologyfaculty
  • neurolres
  • neuropostdocs
  • sbrcseminar

[edit] Computer Science

Send a note to colloq-subscribe-at-cs.stanford.edu to subscribe.

  • Colloq-at-cs.stanford.edu
  • Bac-Coordinators-at-cs.stanford.edu

[edit] Biology

[edit] fMRI/Lucas Center

[edit] Regular seminars

  1. Vision lunch: Wednesday at 11:30 (room 419)
  2. Psychology colloquium Some Wednesdays at 3:45 (room 041)
  3. Cognitive Seminar Fridays at 3:15 (room 050)
  4. FMRI seminar: Occasional Mondays (Bio-X)

[edit] Setting Up Your Computer

Michael Perry is the Systems person in the Vista Lab. New users should coordinate with Michael to get their comptuers set up on the network and for computer needs generally.

[edit] Linux Configuration

The Vista Lab uses Ubuntu to run all software and analyses. Please see the Linux Configuration page for more details regarding packages and settings that are required, or just recommended, in the lab.

[edit] Network Connections

For general information about setting up a network connection please visit the Network Connections page on the Stanford Computing and Communications Site. The site has instructions for setting up a network connection (Ethernet or Wireless) on Windows and Macintosh depending on your connection type and OS. If you don't feel like surfing those pages direct links are provided below.

[edit] Windows
Note: IT Services no longer supports Windows 95, Windows 98, Windows Me, and Windows NT 4.
[edit] Macintosh
Note: IT Services no longer supports Mac OS 9.


For information about service availability and activating your wireless device visit wirelessnet.stanford.edu. Also be sure to see the next section. "Registering a Laptop".


[edit] Registering a Laptop

To activate a wireless card you must first register it. All network devices must be registered in the Stanford network database (NetDB) before they can connect to SUNet. Even if you have already registered your laptop's wired Ethernet connection, you must register your wireless connection separately.

To register a new computer and/or Wireless Card to get an IP Address on the Stanford network (or to update the information for a registered computer), please fill out the form at:

The form asks for the physical addresses for both the wireless and Ethernet connections. To get these in windows go to the command prompt (Start > Programs > Accessories > Command Prompt) and type:

 ipconfig/all 

Note: You must install Windows Critical Updates before filling out the form. To do this you can run Windows Update from your PC using Internet Explorer (not Firefox) or go to the Windows Update web page. This will check for and install all critical updates for your windows machine.

[edit] Creating a guest wireless account:

If you want to create a guest wireless account, for yourself or for a colleague, go to the Guest Accounts Page (SUnet Login required).

Information regarding how such accounts work can be found here (SUnet Login required).

[edit] Essential SUNet Software

When setting up a computer to use the Stanford network certain software is essential (e.g., Anti-Virus).

  • Essential Stanford Software (ESS) is a collection of applications that will help you plug into the Stanford University Network (SUNet) and gain access to Stanford's computing services. ESS includes applications to keep your password secure, protect against computer viruses, send and read email, browse the web, and exchange files.

[edit] Mail settings

Stanford general email and calendar set up page

[edit] Essential Lab Software

To download the software that is specific to our lab please follow the Software link on the main menu.

Information regarding the following requisite software packages is also available on the Software page of this Wiki.
Here are a few direct links:

[edit] Useful Lab Software Utilities

grabit - Matlab function to read data points from a graph

[edit] Adding A Network Printer

You will probably not have a printer directly connected to your computer, thus you will need to add a network printer.

Windows

  1. Go to the Control Panel, Select 'Printers', and then select 'Add Printer.' A welcome screen will appear > Click Next.
  2. Choose 'Local Printer' (this seems odd but windows idea of what a network printer is differs from everyone else's). De-select "Automatically detect and install my Plug and Play Printer". > Click Next
    Print1.png
  3. Select "Create a new port:" Set "Type of port:" to 'Standard TCP/IP Port' >Click Next
    [Image:Print2.png]]
  4. This will take you to a different program "Add Standard TCP/IP Printer Port". Select Next to get past the welcome screen.
  5. Place the printers full name (for example: spectra.stanford.edu, or gingko.stanford.edu) in the Printer Name and Port Name slots. > Click Next > Click Finish
    Print3.png
  6. Select the correct driver for the printer you are adding. > Click Next
    Print4.png
  7. Name the Printer so you know what it is. > Click Next
    Print5.png
  8. Do not share the printer (make sure share is not selected)
  9. Print a test page to see if the printer works. > Next > Finish

[edit] Misc. Linux Setup

[edit] NVIDIA Driver Setup

Run the following shell script:

yum install kmod-nvidia xorg-x11-drv-nvidia-libs.i686
sed -i '/root=/s|$| rdblacklist=nouveau|' /boot/grub/grub.conf
mv /boot/initramfs-$(uname -r).img /boot/initramfs-$(uname  -r)-nouveau.img
dracut /boot/initramfs-$(uname -r).img $(uname -r)
setsebool -P allow_execstack on

Then reboot.

[edit] Windows 7 - The upgrade

Perhaps we could put in instructions here on how to get the disks and licenses.


Set up proxy server for journal access using URL

http://library.stanford.edu/apcproxy/suproxy.pac

There are instructions for setting proxy server on Chrome from UC Davis. The Stanford site has instructions for Firefox and IE.

[edit] 64-bit Windows

If you're using a 64-bit Windows machine there are a couple of know issues with running some lab programs. The known issues are with mrMesh and CINCH. Elsewhere on this WIKI we have provided fixes to these issues. Below you will find links to the pages with those fixes.

[edit] mrMesh
  • For information regarding the issue with mrMesh Server see the DTI page.
[edit] CINCH
  • For information regarding the issue with CINCH see the CINCH page.

[edit] Mapping Network Drives from Unknown IP Address Ranges

[edit] Octave

I installed octave-3.2.4.exe on Windows. Plots and images were a problem. I discovered that on my Windows 7 (32 bit) machine I needed to run

  • pkg unload oct2mat

or else gnuplot.exe hung the program. Apparently, there is some kind of 'famous' oct2mat bug. Here is a link

plotting oct2mat issues


[edit] Tips for converting Presentations between Mac and PC

When making a PowerPoint presentation on an Apple computer, follow these instructions for inserting pictures (even if those pictures are from the web):

Go to the "Insert" menu, choose Picture-->From File...

Choose the file you want, and proceed as normal.

DO NOT simply drag the picture or the file into your PowerPoint presentation, unless you plan only to open it on your computer. Windows and Linux machines will not be able to read images in the presentation (due to a missing QuickTime decompression component) unless you insert it as laid out above.

If you are getting the picture from the Web, save it to a file first, then insert as above.

If you have previously made a presentation by dragging pictures into it and you now want to make the presentation compatible for Windows or Linux (OpenOffice Impress), you can save the individual images in your presentation by right-clicking on the image in your presentation, selecting "Save as Picture..." and then reimporting the image through the insert menu as above. This should fix any problems.

[edit] Printing Posters

There are two options for poster printing as of October 2006:

  • Use the department printer (elder2) – free, anytime, up to 42’’ paper size
  • Use the bio-x poster printer – costs ~27$, fast, time limited, 42’’ paper size

Please follow the instructions below for each.


[edit] 1. Printing a poster on the department poster printer

This poster printer was donated in 2009, and is much easier and faster than the old departmental dinosaur. It lives in the printer room on the 3rd floor. Its name is elder2. To print to it, you will need to take your poster file to the 3rd floor printer room and print from there.

Before you start:

  • Make sure elder2 is ON.
  • If its missing toner or paper notify Peter Smith.
  • If you need to load paper yourself, follow the directions shown on elder2. Tip: Make sure to push the role of paper all the way onto the metal pole so it's flush with the black barrier on the right side.

Sending a poster to elder2 from a printer room PC:

  1. In power point, open your poster, and open the print menu.
  2. Choose elder2 as your printer, and select “scale to fit paper”
  3. Go to “properties” and select orientation (landscape/portrait)
  4. To define the page size, click “Advanced” next to where you selected the orientation. Under paper size, select “PostScript Custom Page Size” and input your desired poster size. Note that the width and height are reversed here, so width actually means how tall your poster is and height means how long it is.
  5. Use print preview to make sure you did everything right.

More notes about elder2:

  • Elder2 prints posters up to 42’’ tall, but only 36’’ paper was available as of March 2009.
  • There were some problems printing to elder2 from the macs in the printer room as of March 2009, so stick to the PCs for now.
  • Notice that some colors might appear slightly differently on Elder. Best to check the main colors you use in a small slip before you send the real poster.


[edit] 2. Printing in the bio-x

There is a brand new poster printer in the third floor of the clark center, next door to Peet’s. The person in Charge is Tanya Raschke. You need to come there once and train with her, give her an account number to charge, and then you can do it yourself, M-F 8am-5pm. A lot of information is in http://clark-it.stanford.edu/poster.htm

Notice that a poster costs about 28$. They will charge twice if you find an error on it. Make sure to ask Tanya to print a receipt for you and give it to Pam.

[edit] Miscellaneous Equipment

==Head-rest/Chin-rest== Can be ordered from Richmond Products. (As per Ricardo Motta, November, 2008.) There was a vision list posting with some useful Head-rest chin-rest links links for head-rests, too.

[edit] Shielded box for MR display

(From David Ress) Alex Huk put together some pictures and sketches at one time that were on one of the old web pages. Those notes were for one of the very earliest designs, using a plastic box with copper foil shielding. That's the only doc about the enclosure design I've ever seen. Maybe if you ask Karlheinz again he'll FINALLY put together some CAD drawings for the thing...

The shielded dislay enclosures that I have used have, lately, all been constructed by your own Karlheinz Merkle in Stanford's Physics shop. I've asked Karlheinz several times to put together a set of drawings for the enclosures, but to no avail. The boxes are presently made entirely from aluminum except for the conductive glass front plate which we still purchase from Tempest Security. Do you intend to build one of these on your own?

[edit] Computational Resources

We have multiprocessor machine (azure) for larger computational jobs. (We are about to add another 48 processor machine). The distribution of activity on these processes can be managed using the Sun Grid Engine that was set up and is being maintained on azure by Kendrick Kay.

In addition, many of the linux workstations in the lab can be used as compute servers as needed. As a courtesy, please give priority to the workstations owner and ask them before launching a big process that is likely to slow them down. We maintain a list of all the lab computers: Computer list.

You can set up guest wireless access from this web-site.

[edit] Data Restore

You can submit a restore request to have a file or folder restored from the back-up servers.

Fill out the form here: http://stanford.edu/group/vista/white/restorerequest.html

[edit] Tips, Tricks & Frequently Ask Questions

Having problems compiling Mex files? Not sure what server is for what? Visit (and update) the Tips, Tricks & FAQs section.

[edit] Writing Documents

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