Wallace:fMRI

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When creating a stimulus array for a rapid event-related fMRI experiment, you'll need to pseudo-randomize the stimulus order in a way that is compatible for deconvolution analysis. The best way to do this is a program called optseq2.
When creating a stimulus array for a rapid event-related fMRI experiment, you'll need to pseudo-randomize the stimulus order in a way that is compatible for deconvolution analysis. The best way to do this is a program called optseq2.
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== Data Analysis ==
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== AFNI ==
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=== Getting raw data from the scanner ===
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After a scan you will need to get the data from the scanner to our server.
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=== AFNI ===
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[http://afni.nimh.nih.gov/afni/ AFNI] is a software package for processing, analyzing, and displaying fMRI data. It is freely available from the NIH. You can find the latest version at
[http://afni.nimh.nih.gov/afni/ AFNI] is a software package for processing, analyzing, and displaying fMRI data. It is freely available from the NIH. You can find the latest version at
   http://afni.nimh.nih.gov/afni/download/afni/releases/latest
   http://afni.nimh.nih.gov/afni/download/afni/releases/latest
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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".
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".
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= Set up =
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=== Set up ===
You'll need to update your .cshrc file in order to have all the correct paths set when you open terminal. To open your .cshrc file, enter the following command into terminal:
You'll need to update your .cshrc file in order to have all the correct paths set when you open terminal. To open your .cshrc file, enter the following command into terminal:
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= Updating =
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=== Updating ===
Many problems can occur if your afni verion is not up to date. To update, first type the following command into terminal:
Many problems can occur if your afni verion is not up to date. To update, first type the following command into terminal:
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Finally, after you update you must enter the command
Finally, after you update you must enter the command
   rehash
   rehash
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== Data Analysis ==
 +
=== Getting raw data from the scanner ===
 +
After a scan you will need to get the data from the scanner to our server.

Revision as of 13:21, 30 January 2014

Wallace Lab


Contents

Experiment Design

Creating Code

When creating a stimulus array for a rapid event-related fMRI experiment, you'll need to pseudo-randomize the stimulus order in a way that is compatible for deconvolution analysis. The best way to do this is a program called optseq2.

AFNI

AFNI is a software package for processing, analyzing, and displaying fMRI data. It is freely available from the NIH. You can find the latest version 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".

Set up

You'll need to update your .cshrc file in order to have all the correct paths set when you open terminal. To open your .cshrc file, enter the following command into terminal:

 open -e ~/.cshrc


Updating

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


Data Analysis

Getting raw data from the scanner

After a scan you will need to get the data from the scanner to our server.