The "Vertex Analysis: requires you to prepare two sets of files: individual segmented structures combined into one file, and a design matrix and t and f contrasts saved as a set of files.

Combining individual files: concat_bvars

Outcome: a single file that contains all studies' bvars 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

Create the single file with this command: concat_bvars output_name.bvars [list of ".bvars" files]. You most likely will use a wildcard "*" rather than typing each filename. For example, to combine all the left hippocampus files in the directory: [user@localhost temp]$ concat_bvars L_Hipp_all.bvars con*-L_Hipp_first.bvars dis*-L_Hipp_first.bvars

This command will combine ALL individuals' L_Hipp files. Therefore, if you want to exclude a subject, you need to move the files out of the folder, and re-run concat_bvars. You may want to name the output file with the number of subjects, e.g., "L_Hipp_all_N35.bvars" for 35 subjects.

The files will be ordered alphabetically; knowing the order is required for the later steps (specifically, creating the design matrix).

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 need to be 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, 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/

2) Open a terminal in this "design folder"

3) Open 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).

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.

You will copy the design folder, including all the files, to subfolders of each structure you analyze.

Tip: Glm from FSL GUI

Type "fsl" to start the FSL GUI, click "Misc " then "GLM Setup".

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