Differences between revisions 4 and 5
Deletions are marked like this. Additions are marked like this.
Line 11: Line 11:

There are numerous examples worked out [[FsgdExamples|here].<<BR>>
Line 29: Line 31:
* CLASS only needs the class name (case is ignored), the next two
items will be used in the display.<<BR>>
* The third input is ignored.<<BR>>
* CLASS only needs the class name, the next two items (eg, "plus blue"
will be used in the display.<<BR>>  
* The third input is ignored because of the hash (#).<<BR>>

This page describes the FreeSurfer Group Descriptor (FSGD) File Format (Version 1) as of 11/12/02. FSGD is a way to describe a group of subjects and their accompanying data. This can include class membership and other continuous varibles (eg, age). The nice thing about the FSGD is that various FreeSurfer programs can automatically compute the design matrix from an FSGD file. The FSGDF is used by mri_glmfit, tksurfer, tkmedit. They are created automatically by qdec, but qdec is currently (12/9/08) limited to two continuous variables and two discrete variables. The FSGD format uses tags to identify information.

There are numerous examples worked out [[FsgdExamples|here].

Example of a legal file:

  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

Notes:
* The first line must be "GroupDescriptorFile 1".
* Title is not necessary. This will be used for display.
* CLASS only needs the class name, the next two items (eg, "plus blue" will be used in the display.
* The third input is ignored because of the hash (#).
* 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 (ie, blank or tab).
* Any line where # appears as the first non-white space character is ignored (ie, a comment).
* 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.
* The 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.

FsgdFormat (last edited 2009-05-29 14:11:26 by NickSchmansky)