The "Vertex Analysis: requires you to prepare two sets of files: the individual segmented structures combined into one file, and a design matrix to indicate which file belongs to which groupand t and f contrasts saved as a set of files.
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Combining individual files: concat_bvars
Outcome: a single file that contains all studies' bvars files, for a given structure.
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(An older version of these instructions is here, in case yuo do not have the variable files.)
Before you start, make sure you have opened the variable file (e.g., "...\LinuxShare\FIRST\ID99N20G2\varfiles\allvariables.txt"). Follow these steps in Linux (unless other specified):
1) Create a folder for this design
Either using the File Browser or the mkdir command in the terminal, create a folder.
By default, create a top-level folder called "designs," and subfolders for each design under that. Suggested convention is illustrated by these examples :
.../LinuxShare/FIRST/ID99N20G2/designs/2sample/
.../LinuxShare/FIRST/ID99N20G2/designs/2group_covage/
.../LinuxShare/FIRST/ID99N20G2/designs/1group_covagesex/
.../LinuxShare/FIRST/ID99N20G2/designs/correlationage/
.../LinuxShare/FIRST/ID99N20G2/designs/correlationage_covsex/
.../LinuxShare/FIRST/ID99N20G2/designs/regressionageAHI_covsex/
Either start from the FSL GUI (if so, open fsl in the design folder), or from a terminal "cd" to the directory, and type Glm (case sensitive).
Example:
4) Select "Higher-level / non-timeseries design" from the pull-down menu.
5) Enter the number of studies (# inputs).
6) Enter the number of variables in your design as number of EV's.
"EV's" at the top of the GUI, not voxel-dependent EV's at the bottom. This will add that number of columns to the design. Do not count the "Group" column in the GUI (the group variable must be pasted as an EV).
7) Click "Paste," then "Clear"
8) In Windows, open the allvariables.txt in Excel. Select the data (not headers) you want to use for the design.
"Hide" columns to skip them; the columns must be contiguous, but you can exclude those on the left or right.
9) In Linux, click in the empty "Paste" window, and click Ctrl^Y to paste the values. Click OK.
Ctrl^V does not work, for some odd reason. Right-click does not give a Paste option either. Remember to paste the group variable along with other variables.
10) Enter the column names.
12) Click "Contrasts & F-tests" tab.
13) Create contrasts:
To compare the means of two samples, set both Contrasts and F-tests to 1. Make sure the box next to C1 is selected (it should be yellow). Select the F1 box.
11) 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 use des_[folder name] using the name of the design folder). 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.
Tip: Glm from FSL GUI
Type "fsl" to start the FSL GUI, click "Misc " then "GLM Setup".
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