Wallace:Lab Notebook: Difference between revisions
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=== XCode and Terminal === | === 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. | 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 === | ||
Revision as of 07:29, 19 May 2014
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Wallace Lab
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General Important NotesPrinting/ScanningContact InformationInstalling SoftwareIf 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 TerminalIf 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. FreeSurferFreeSurfer 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. GrantsHere's some general information about applying for grants/fellowships. NRSAAt 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. |
