These are CV as they come from the contrasts. Contrasts are simply a
linear combination (addition or subtraction) of the PE or beta images.
PSC requires dividing by the constant term.
I always use the CV and I also use the above AFNI commands.
The one cautionary note is that AFNI/SPM have the L and R on opposite
sides, so you want to make sure your extracting from the correct
voxels. Additionally, you don't need step 2 as AFNI can read .nii
files.
Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General
Hospital and Harvard Medical School
Office: (773) 406-2464
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On Sat, Feb 12, 2011 at 11:27 PM, Yang Hu <[log in to unmask]> wrote:
> Dear Experts,
>
> Based on whole-brain analysis via SPM8 (1st- and 2nd-level analysis), I want to extract signal value from atlas-based ROIs (e.g. amygdala) in four experimental conditions, compared with rest condition respectively, by AFNI rather than MarsBar. Specific steps are listed as follows:
>
> 1. Mask generation: by WFU pickatlas, an file of ROI in amygdala (named as "amy.nii") was generated
> 2. File conversion: by AFNI command "3dcopy", the "amy.nii" was converted to "amy+orig.BRIK/HEAD", which could be recognized by AFNI
> 3. ROI calculation: by AFNI command "3dmaskave", the average value within the ROI mask (amygdala) of each subject (sbj**) in certain condition (con_000*) could be obtained; Specifically, the full command is like that "3dmaskave -quiet -mask amy+orig sbj**_con_000*.hdr". The file "sbj**_con_000*.hdr" was generated after 1st-level analysis via SPM8.
>
> So I just wonder the meaning of ROI value obtained through those steps mentioned above. Whether does the value mean percent signal change (PSC), contrast value (CV), or parameter estimates (PE) ? And what's the difference between the three terms (namely PSC, CV, PE) always used in ROI analysis?
>
> Thanks a lot for your help and comment!
>
> Yang Hu
>
> ICN, ECNU, Shanghai, China
>
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