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In brief: Create a model with FSL's "Glm" function, using "allcovariatestable.txt" in the "varfiles" subfolder of the FSL FIRST folder; open in Excel, select the variables, and paste into the Glm GUI.
Example: V:\LinuxShare\FSL_FIRST\ID111N1045G2\varfiles\allvariablestable (Text Document)
Design matrix and contrast files
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.../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/
2)
OpenFrom Linux, open a terminal in this
"new design folder
".
3)
OpenRun "Glm"
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).
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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). In other words, if for example you are looking at group, age and sex, you should have 3 EV's.
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.
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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.
If you have more than one cariable, create a separate F contrast for each one. Additionally, create an all-effects F contrast (e.g., for 3 EV's, 1 0 0/0 1 0/0 0 1). Here is an example with group + 3 covariates - F5 is the "all-effects" F contrast (we can use this to determine fit of the model).
11) Save the file
Under the GLM Setup window click Save, navigate to the directory with the files, and if you are using CSPM save as "design". Otherwise, if you are doing manual analyses, 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.
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Tip: Glm from FSL GUI
Type "fsl" to start the FSL GUI, click "Misc " then "GLM Setup".
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