The "Vertex Analysis: requires you to prepare two files: the individual segmented structures combined into one file, and a design matrix to indicate which file belongs to which group.
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Combining individual files: concat_bvars
Outcome: a single file that contains all studies' files, for a given structure.
In a terminal, navigate to the directory with all the bvars files, e.g., [user@localhost temp]$ cd /mnt/hgfs/LinuxShare/temp
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Design matrix and contrast files
Outcome: a group of files than are used to run statistical analyses; these are not specific to a structure (and so can be copied across structures to repeat the same analysis).
The design matrix is common to FSL statistical routines, and is the same as created in SPM. However, for FIRST there are some differences (see "Create a design matrix" in guide). Specifically, the group should be in one rather than two columns, and F tests should need to be used. Follow these steps:
1) Open Glm
Either start from the FSL GUI, or from a terminal "cd" to the directory, and type Glm (case sensitive).
2) Enter the total number of subjects, and the number in the first group (if using a two-group design)
Select "Higher-level / non-timeseries design" from the pull-down menu, enter the number of subjects (# inputs), click Wizard, select "two groups, unpaired", enter the number of subjects in group 1, click Process.
3) Adjust the design to have one column for group
Go the to General Linear Model window, and set to 1 EV; the Group B column will disappear.
4) Change the second group EV value from 0 to "-1"
Scroll down to the second group (where values change from 1 to 0 in EV1 column); change all the "0"'s to "-1" (tedious).
5) Set one T contrast and one F contrast
From the top of the General Linear Model window select the "Contrasts & F-tests" tab, and set to one Contrast, one F-test, and select the C1 contrast for the F1 (click on the small square).
6) Save the file
Under the GLM Setup window click Save, navigate to the directory with the files, and choose a descriptive name ("des_2sample" for example). You can ignore the warning.
This will save a number of files, as in the example below (where "des" was chosen as the name). These files are used as input to several of the following procedures.
Other designs (covariate, more groups)
Moving the files to a separate folder
Because the stats only needs the design matrix and combined all.bvars files, these can be copied to subfolders for the next stages; this helps keep everything organized. Since you will likely be doing multiple models and statistical analyses, you can create as many well-named folders as you like, and copy the same set of design matrix & all.bvars files.
Background on design matrix
The design matrix is a text file with header information and numbers in columns. By tradition, the file is saved with a name like "design.mat". Each row represents a subject, in the order stored in the concatenated bvars file. The simplest design matrix (for a two group dataset) is a single column, with +1 for group 1 and -1 for group 2. A default matrix created by Glm for two groups includes two columns, but this is not what is needed for FIRST. There is also header information which includes the number of columns (I think), the number of subjects, and the maximum value of each column. For example, here is a two-group, 5 subjects/group design matrix:
created. Furthermore, the file format is different in SPM and FSL: in FSL, there is a custom design matrix, and t-contrast and f-contrast files are created at the same time as the design matrix. This is different to SPM where the design is specified, then any t or f contrast can be created from that design.
(An older version of these instructions is here.)
Follow these steps:
Glm from FSL GUI
Type "fsl" to start the FSL GUI, click "Misc " then "GLM Setup".
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