When you run isxconcat-sess add -paired-diff. This will compute 1-2 for each subject. You can then run mri_glmfit. With that FSGD file, your contrast should be 1 not 1 0 doug

On 2/6/16 11:17 AM, Thục Trinh wrote:

Hello,

I'm working on group analysis in fMRI activation using FSFAST. I tend to test whether any significant changed in fMRI activation within group across two time points ( pre-training vs post). I ran first level already. I still confuse about the concat data and the mri_glmfit command. Here are the command lines, I'm wondering if it runs exactly what I want it to do.

-- idlist

Input NCP140005_1 Input NCP140005_2 Input NCP140012_1 Input NCP140012_2 Input NCP140071_1 Input NCP140071_2 Input NCP140079_1 Input NCP140079_2 Input NCP140082_1 Input NCP140082_2 Input NCP140543_1 Input NCP140543_2 Input NCP140556_1 Input NCP140556_2 Input NCP140558_1 Input NCP140558_2

-- concat data isxconcat-sess -sf idlist -analysis work.sm5.lh -contrast con-v-arrow -o group2

-- FSGD file

GroupDescriptorFile 1 Title Con-arrow Gr2 Class Defi Input NCP140005 Defi Input NCP140012 Defi Input NCP140071 Defi Input NCP140079 Defi Input NCP140082 Defi Input NCP140543 Defi Input NCP140556 Defi Input NCP140558 Defi

-- run glm analyisis

mri_glmfit --glmdir lh.paired.gr2-diff --y ces.nii --fsgd con-arrow_group2.fsgd --C mean.mat

-- content in matrix contrast C = [ 1 0 ]

Thank you, Trinh

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