Wallace:Lab Notebook: Difference between revisions

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== Installing Software ==
== Installing Software ==
If you need to install new software (Adobe Illustrator, EndNote, Matlab, etc.), software ISOs can be found on bluearc under "Drivers and Software". If we don't have a valid license number anymore we may need to purchase a new one.
If you need to install new software (Adobe Illustrator, EndNote, Matlab, etc.), software ISOs can be found on bluearc under "Drivers and Software". If we don't have a valid license number anymore we may need to purchase a new one. Software programs specific to a particular technique are under the appropriate tab.
 
=== XCode and Terminal ===
If you would like to analyze fMRI data with AFNI, you will need to set up XCode and terminal. The following instructions are for a Mac computer. In terminal, we first need to change the shell. Open a terminal window, then go to Terminal > Preferences on the menu bar. Under the Startup tab, go to Shells open with: section. Click Command and type:
  /bin/tcsh
 
and then close the window. Terminal will now open with tcsh instead of bash.
 
=== FreeSurfer ===
FreeSurfer is an open source software package that is used in conjunction with other neuroimaging programs to analyze MRI data. Our main use will be the program optseq (for creating optimally randomized stimuli sequences for fMRI) and reconall (for cortical surface reconstruction). '''The following instructions are for a Mac computer.''' To download FreeSurfer, go here:
  https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
First you'll need to get a FreeSurfer license. Happily, it's free. Click on Registration and go through the instructions. The license will be e-mailed to you.
 
The license file you get is actually a piece of text that you are to copy into a text file and save as '.license' under the $FREESURFER_HOME environment variable. To set that, you next need to download FreeSurfer (from the original link, click on Download). Download the package appropriate for your operating system. It's a big file (a few GB's) so it might take a while. Go get a coffee.
 
After you've finished installing it, you should see the freesurfer folder under Applications. Next, we need to make sure the computer can be directed to the location of freesurfer. The best way to do this is the .cshrc file. To open yours, go to the terminal window and type:
  open -e $HOME/.cshrc
 
If no such file exists, type:
  touch $HOME/.cshrc
 
After this you should be able to open the file with the command line listed above. Copy paste the following lines into your .cshrc file:
  setenv FREESURFER_HOME /Applications/freesurfer
  source $FREESURFER_HOME/SetUpFreeSurfer.csh
 
There will be other lines you'll need in your .cshrc file to direct to other programs, they should be listed in the section of this wiki about that program.
 
To test that everything is working correctly, type:
  which freesurfer
 
and the response should be the location of the freesurfer folder.


== Grants ==
== Grants ==

Latest revision as of 12:53, 19 May 2014

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Wallace Lab



General Important Notes

Printing/Scanning

Contact Information

Installing Software

If you need to install new software (Adobe Illustrator, EndNote, Matlab, etc.), software ISOs can be found on bluearc under "Drivers and Software". If we don't have a valid license number anymore we may need to purchase a new one. Software programs specific to a particular technique are under the appropriate tab.

Grants

Here's some general information about applying for grants/fellowships.

NRSA

At some point you'll likely work on an F31 (pre-doctoral NRSA) or F32 (post-doctoral NRSA). The NIH provides this 1992 style graphic to understand the difference between the two: 

 http://grants.nih.gov/training/FTAwards.htm

Below are some resources that might be helpful during the preparation and submission of your NRSA grant.

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