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|=== pre-smoothed files ===||=== pre-smoothed fsaverage surfaces ===|
Qdec is a single-binary application included in the Freesurfer distribution. QDEC is an acronym for Query, Design, Estimate, Contrast. It is intended to aid researchers perform inter-subject / group averaging and inference on the morphometry data (cortical surface and volume) produced by the Freesurfer processing stream. Prior to usage of qdec, all subcortical segmentation and surface reconstructions for all subjects in a study must be complete. The 'recon-all' script performs that work, and is not the subject of this document.
The qdec binary is a GUI front-end to a 'statistics engine' (the mri_glmfit binary, included in Freesurfer, currently fills this role) intended to:
- select the subjects meeting the criteria under study
- generate the necessary input to the stats engine, which, for mris_glm, includes:
a Design matrix (called X in the GLM equation) containing the explanatory variables,
a parameter Estimate matrix (called A in the GLM equation), and
the Contrast vector(s)
- generate and optionally display the output data and/or images
Without the aid of the qdec tool, a researcher has to manually perform the stats analysis, which, when using the mri_glmfit utility, requires manual creation of an 'FSDG' file which specifies the X and A matrices for the group of subjects under study, and manually specifying the contrast vector(s) for the hypothesis to test. This can be quite tedious, and greatly slows down the "Test for an effect of factor X" research task. This is, in fact, the procedure described in the [wiki:FsTutorial/GroupAnalysis 'Group Analysis' tutorial].
Prior to using the qdec application, your group subject data must be processed by the standard Freesurfer processing stream, via the recon-all script. [http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial A freesurfer tutorial is available.] This processing stream supplies the surfaces and morphometry data on each subject.
pre-smoothed fsaverage surfaces
Qdec is happiest if there exists for each subject pre-computed smoothing data for the fsaverage target surface for each measure (thickness, sulc and curv). There are two options to create this data, via recon-all, or, if the cluster machine 'seychelles' is available to you (at the NMR Center), the script run_mris_preproc.
The recon-all incantation is:
recon-all -s <subjid> -qcache
The -qcache flag will spawn numerous (30+) parallel mris_preproc processes on the machine, so be prepared for it to consume 100% for almost an hour.
If the cluster machine is available to you, then:
ssh seychelles $ cd $SUBJECTS_DIR $ source /usr/local/freesurfer/nmr-dev-env $ run_mris_preproc qdec.table.dat
The qdec.table.dat is a text file associated with your group of subjects, described next.
The primary input to qdec is a text file, named qdec.table.dat, containing the subject IDs, and discrete and continuous factors, in table format. Here is an example file:
fsid gender age diagnosis Left-Cerebral-White-Matter 011121_vc8048 Female 70 Demented 202291 021121_62313-2 Female 71 Demented 210188 010607_vc7017 Female 73 Nondemented 170653 021121_vc10557 Male 75 Demented 142029 020718_62545 Male 76 Demented 186087 020322_vc8817 Male 77 Nondemented 149810
For each discrete factor, there must exist a file named <factor>.levels which lists all possible levels. For example, accompanying the example qdec.table.dat file must be a file named 'gender.levels' containing these lines:
and there must be a file named 'diagnosis.levels' containing these lines:
Of course you may have different discrete factor names and levels (or even no discrete factors, in which case all column data is assumed to be continous factors).
SUBJECTS_DIR and FREESURFER_HOME
First, set your SUBJECTS_DIR environment variable to point at your group subjects directory:
setenv SUBJECTS_DIR /space/boing/users/me/subjects/my_big_study
Or, there is a sample data set you can use to learn:
setenv SUBJECTS_DIR /autofs/space/sake_025/users/nicks/subjects/qdec3
Then, setup the 'dev' Freesurfer environment, which contains qdec:
For display purposes, you will need to have an average subject included in this subject group. Freesurfer's fsaverage will do fine:
cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage
Now start qdec:
The first thing you will need to do is to load your qdec.table.dat file. Click File -> Load Data Table and traverse to your subjects directory and select your qdec.table.dat file that you created. When you click Open, it should load your file, the contents scrolling-by in the terminal window. If the data is loaded correctly, you should see in the terminal window a summary, like this example:
Number of subjects: 295 Number of factors: 201 (2 discrete, 199 continuous) Number of classes: 4 Number of regressors: 800
Your discrete and continous factors should appear in the Design tab of the qdec application.
Select up to four factors in the Design tab to regress against. For the example data, you could select 'gender', 'diagnosis' and 'age'. Leaving the 'Smoothness', 'Measure' and 'Hemisphere' at their defaults (10mm, thickness, and lh), clicking the 'Analyze' button will begin the stats processing, executing the mri_glmfit executable. Upon clicking 'Analyze', the terminal will display the output of this processing. Also, progress information is shown in the bottom bar of the qdec application.
Once the analysis is complete (taking up to several minutes for a large subject set), the fsaverage inflated surface will appear in the display window. Now click on the 'Display' tab. You will see displayed in the form of questions a summary of the various analyses that were completed. Click on one of these questions to load those results. Here is an example display:
Notice the green cross-hairs. You can display a plot of the data for a particular vertex by right-clicking on a point while holding-down the Ctrl key. Here is an example plot that corresponds to the shown selected vertex:
Notice that thickness correlates with age at this vertex (thinning occurs).
To rotate the display, hold-down the right mouse button while moving. It takes quite a bit of practice to learn how to move the display. Holding-down the middle button while moving the mouse will move the display. Holding-down the left mouse button while moving will zoom the display.