Dear Guillaume,
Thank you for your help, it helps me understand more about masking.
After looking into 'spm_fmri_spm_ui.m', I understand the threshold is basically calculated by three components: "SPM.xGX.rg", "SPM.xGX.GM", and "SPM.xGX.gSF". But the first component "SPM.xGX.rg" is calculated by spm_global.m, which has only one line code "error('spm_global.c not compiled - see Makefile')".
The information in the comments of spm_global.m is as follows:
%__________________________________________________________________________
%
% spm_global returns the mean counts integrated over all the
% slices from the volume.
%
% The mean is estimated after discounting voxels outside the object
% using a criteria of greater than > (global mean)/8.
%
%____________________________________________________
- I tried to reproduce this step in the Auditory fmri example (Manual of SPM8, ch28) by R
- the dimension of auditory data is 79*95*68 with 84 images (or scans)
- If the storage of this data is an array with dimension [79,95,68,84]
As my understanding for this paragraph, the first value of rg should be:
# select the first of 84 images
y1 = y[,,,1]
# discount voxels by the criteria of greater than (global mean)/8
y2 = subset(y1, y1>mean(y1)/8)
# the mean of y2 is equal to the first value of rg
mean(y2)
But the result is not correct (compared to the SPM.xGX.rg), would you please help me ?
many thanks
Philip Lin
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