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| [wiki:Self:FsTutorial top] | [wiki:Self:FsTutorial/GroupAnalysis previous] | [[FsTutorial|top]] | [[FsTutorial/GroupAnalysis|previous]] |
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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. | |
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| 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: | The FSGDF format uses tags to identify information, as shown below (this is just for example, and not something that can be made from the tutorial data): |
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| cd $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/group_analysis_tutorial/stats }}} attachment:demoTable2.jpg {{{ As previously shown, an example of a legal file: |
Example of a legal file: |
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| Class Class1 plus blue CLASS Class2 circle green SomeTag |
Class Class1 plus blue Class Class2 circle green |
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| Input subjid1 Class1 10 100 1000 | Input subjid1 Class1 10 100 1000 |
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Notes: |
Notes: |
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| * The third input will be treated as a comment, due to the ''#'' at the beginning of the line. | * The third ''Input'' tag will be treated as a comment, due to the ''#'' at the beginning of the line. |
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| * ''Some``Tag'' is not a valid tag, so it will be ignored. | |
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| General Rules: | General rules: |
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| * Tags are NOT case sensitive. * Labels are case sensitive. |
* Tags are NOT case sensitive (for instance, 'Class' and 'CLASS' are the same tag). * Labels are case sensitive (for instance CLASS1 and Class1 are NOT the same label). |
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| * A class marker can optionally be followed by a class color. | * A class marker can optionally be followed by a class color.<<BR>> |
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| 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. |
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| A correct FSGD file is presented [wiki:Self:FsTutorial/CorrectFsgdFile here] for comparison. |
Create an FSGD file
The FSGDF format uses tags to identify information, as shown below (this is just for example, and not something that can be made from the tutorial data):
Example of a legal file: ------------------------- cut here ------------------ GroupDescriptorFile 1 Title MyTitle Class Class1 plus blue Class Class2 circle green 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 tag will be treated as a comment, due to the # at the beginning of the line.
DefaultVariable is the default variable for display.
General rules:
- Tags are NOT case sensitive (for instance, 'Class' and 'CLASS' are the same tag).
- Labels are case sensitive (for instance CLASS1 and Class1 are NOT the same label).
- 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.