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 *To follow this exercise exactly be sure you've downloaded the [wiki:Self:FsTutorial/Data tutorial data set] before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names.

[wiki:FsTutorial top] | [wiki:FsTutorial/GroupAnalysis previous]

  • To follow this exercise exactly be sure you've downloaded the [wiki:FsTutorial/Data tutorial data set] before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names.

Create an FSGD file

Given the following study variables in a spreadsheet, compose an FSGD file with the appropriate variables in order to specify a design matrix that can be used to examine the relationship between a subject's age and cortical thickness. To do this, open the text editor of your choice and add individual tags by following the general example and rules prescribed in the previous page (and provided again below for convenience). In general, it's a good idea to name the file something intuitive, such as my_gender_age_fsgd.txt. To create your FSGD file you first need to change to the directory you'd like to create the file in:

cd $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/group_analysis_tutorial/stats

attachment:demoTable2.jpg

  As previously shown, an example of a legal file:
  ------------------------- cut here ------------------
  GroupDescriptorFile 1
  Title MyTitle
  Class Class1 plus blue 
  CLASS Class2 circle green
  SomeTag
  Variables             Age  Weight   IQ
  Input subjid1 Class1   10    100   1000               
  Input subjid2 Class2   20    200   2000
  #Input subjid3 Class2   20    200   2000
  DefaultVariable Age
  ------------------------- cut here ------------------

Notes:

  • The first line of the file must be "GroupDescriptorFile 1".

  • Title is not necessary. This will be used for display.

  • Class only needs the class name, the next two items, if present, will be used in the display.

  • The third input will be treated as a comment, due to the # at the beginning of the line.

  • DefaultVariable is the default variable for display.

  • SomeTag is not a valid tag, so it will be ignored.

General Rules:

  • Tags are NOT case sensitive.
  • Labels are case sensitive.
  • When multiple items appear on a line, they can be separated by any white space (i.e., blank or tab).
  • Any line where # appears as the first non-white space character is treated as a comment (ignored).
  • The Variables line should appear before the first Input line.

  • All Class lines should appear before the first Input line.
  • Variable label replications are not allowed.
  • Class label replications are not allowed.
  • Subject Id replications are not allowed.
  • If a class label is not used, a warning is printed out.
  • DefaultVariable must be a member of the Variable list.

  • No error is generated if a tag does not match.
  • Empty lines are OK.
  • A class label can optionally be followed by a class marker.
  • A class marker can optionally be followed by a class color.

Upon completion, save the FSGD file, which can be viewed in the xterm by typing:

cat my_gender_age_fsgd.txt

in the directory where it has been saved.

A correct FSGD file is presented [wiki:FsTutorial/CorrectFsgdFile here] for comparison.

FsTutorial/CreateFsgdFile (last edited 2008-04-29 11:46:13 by localhost)