Wallace:Lab Notebook: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
Line 79: Line 79:


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.
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.
You'll also need a license to run FreeSurfer. Happily, it's free. Go to the Registration tab under the download link listed above and fill out the form. You should receive an e-mail with text that you need to copy into the license file. This part is a little tricky. First, open a text file called .license:
  touch .license
  open -e .license
Copy and paste the 3 lines from the FreeSurfer registration e-mail into this text file. Files that start with a . are a bit tricky because they are hidden if you tried to find them in the finder window. Next we need to move the .license file to the right folder (set by $FREESURFER_HOME).
  cp .license $FREESURFER_HOME
If you run into a 'Permission denied' error,


To test that everything is working correctly, type:
To test that everything is working correctly, type:

Revision as of 08:45, 19 May 2014

<html><style type='text/css'> .tabs { 

 width: 640px;
 font-family: arial;
 color:#ffffff;

}

.tabs strong{ 

 color: #851e21;

} </style></html>

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.

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.

If you want you can also go to the Settings tab of the Preferences pane and change the colors of the terminal window. Some people find a dark background with white text more eye friendly. Click your desired color scheme then press default.

It's a good idea to have a .cshrc file, which will help you set up your path every time you open terminal. If you don't already have one, you can create one with the following command 

 touch ~/.cshrc

If you've already created a .cshrc file, enter the following command into terminal: 

 open -e ~/.cshrc

The following path commands are good to have in your .cshrc file. Be sure to double check that these path locations are where each program is located on your computer, and make adjustments as needed. 

 set path = ( $path /sw/bin /Applications/AFNI/ /Applications/MATLAB_R2011a.app/bin)
 setenv DYLD_FALLBACK_LIBRARY_PATH /Applications/afni

If you have a different version of Matlab, be sure to change the MATLAB folder as appropriate. Any time you make changes to your .cshrc file, these changes will only apply to "new" terminal windows. If your problem isn't solved after you make .cshrc changes, be sure you're working in a new window.

AFNI

AFNI is a software package for processing, analyzing, and displaying fMRI data. It is freely available from the NIH. Other packages for fMRI data analysis exist, but Sarah can't help you with them.

It's a good idea to get AFNI up and running before you begin data collection and analysis. You can download the latest version of AFNI at 

  http://afni.nimh.nih.gov/afni/download/afni/releases/latest

When the file finishes downloading, you will need to double click the file to un-zip the tar file. Drag the newly created folder to the Applications directory. To more easily access the folder, rename it "afni".

Next you'll need to download XQuartz since X11 is no longer automatically included in new Mac operating systems. You can download it here 

 http://xquartz.macosforge.org/landing/

You'll need to log out and then log back in to make XQuartz the default X11 app. When you log back in, open terminal and simply type the command 'afni'. This should launch AFNI.


Updating AFNI

Many problems can occur if your afni verion is not up to date. To update, first type the following command into terminal: 

 afni -version

If your afni version is more than a month old, it's time to update. To update, type: 

 @update.afni.binaries -defaults

Finally, after you update you must enter the command 

 rehash

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). Their download page also includes a wiki that may help with troubleshooting if necessary. To download FreeSurfer, go here: 

 https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

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.

You will also need to add FreeSurfer to your .cshrc file. You can do so with the following commands: 

 echo ‘setenv FREESURFER_HOME /Applications/freesurfer‘ >> ~/.cshrc
 echo ‘source $FREESURFER_HOME/SetUpFreeSurfer.csh' >> ~/.cshrc

You'll note that there are multiple ways to add text to the .cshrc file, either directly through the terminal window or by manually opening the file. Both ways work, it just depends on what you're comfortable with.

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.

You'll also need a license to run FreeSurfer. Happily, it's free. Go to the Registration tab under the download link listed above and fill out the form. You should receive an e-mail with text that you need to copy into the license file. This part is a little tricky. First, open a text file called .license: 

 touch .license
 open -e .license

Copy and paste the 3 lines from the FreeSurfer registration e-mail into this text file. Files that start with a . are a bit tricky because they are hidden if you tried to find them in the finder window. Next we need to move the .license file to the right folder (set by $FREESURFER_HOME). 

 cp .license $FREESURFER_HOME

If you run into a 'Permission denied' error,

To test that everything is working correctly, type: 

 which freesurfer

and the response should be the location of the freesurfer folder.

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.

Retrieved from "https://openwetware.org/mediawiki/index.php?title=Wallace:Lab_Notebook&oldid=793982"