To view group differences in mricron:
- Open the *_corrp_fstat1.nii.gz in mricron
- Set the range to start from 0.95
- Open *_glm_cope_tstat1.nii.gz
- Make sure Yoke is set in mricro (Window menu)
- In the corrp_fstat1 file, move the cursor to a non-zero location >0.05 (a significant voxel)
- Look at the value in glm_cope_tstat1; this is the size in voxel dimensions of the effect. For example, if the cope is 0.5 and the image resolution is 1mm^3, the the group effect is an increase of 0.5mm outward expansion at that voxel.
- This assumes that the control group is "1" and the patient group "2" in the design matrix.
Details
The "-glm_output option in randomise creates model estimates. The beta's are *_glm_pe_tstat1.nii.gz", where "pe" = "parameter estimates". We are usually interested in contrast parameter estimates ("cope"), so "_glm_cope_tstat1.nii.gz". The pe files will have one value (volume) per parameter in the model, whereas the cope files will have a single value corresponding to the contrast. For example, if you have group, age and sex, you will get files like below, where the "pe" files have three volumes each:
...
- Say you have a contrast C = [1 -1 0]', and for a certain voxel, you have beta = [1 4 2]'. The COPE is simply C'*beta = [1 -1 0] * [1 4 2] = 1*1 -1*4 + 0*2 = -3. This is what goes in the numerator of the t statistic.
- - The *pe* are the parameter estimates, also known as betas (this image has as many volumes as regressors in the design);
- The *cope* are the contrasts of parameter estimates, one image per contrast. It's the inner product between the contrast vector and the betas;- Because the *pe* are estimates, so are the *cope*. These estimates have an uncertainty surrounding them, and the variance around these estimates is the *varcope*;- The *sigmasqr* is the variance of the residuals. The sigmasquareds volume is the unbiased estimate of the noise standard deviation in the GLM.
To view group differences in mricron:
- Open the *_corrp_fstat1.nii.gz in mricron
- Set the range to start from 0.95
- Open *_glm_cope_tstat1.nii.gz
- Make sure Yoke is set in mricro (Window menu)
- In the corrp_fstat1 file, move the cursor to a non-zero location >0.05 (a significant voxel)
- Look at the value in glm_cope_tstat1; this is the size in voxel dimensions of the effect. For example, if the cope is 0.5 and the image resolution is 1mm^3, the the group effect is an increase of 0.5mm outward expansion at that voxel.This assumes that the control group is "1" and the patient group "2" in the design matrix.
To check your variables:
Open Notepad, and drag file the "design.mat" into the application. (This is listed as "MATLAB Data" but is a text file.) You will see columns for each variable. Here is an example with group, age and sex:
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