Hi Doug,

In order to run surface based analysis on PET maps, I used the following steps:

1. Co-registering SUVR to T1

bbregister --s name --mov suvr.nii --bold --init-fsl --reg reg.dat --o suvr_T1.mgh

2. Concatenate SUVR maps

mris_preproc --target fsaverage --hemi lh --iv subject1/suvr/suvr_T1.mgh subject1/suvr/reg.dat  --iv subject2/suvr/suvr_T1.mgh subject2/suvr/reg.dat --iv … --projfrac 0.5 --out lh.suvr.mgh

3. Smoothing(sm)

mri_surf2surf --hemi lh --s fsaverage --fwhm 10 --cortex --sval  lh.suvr.mgh --tval lh.suvr.sm10.mgh

4.Group analysis (GLM)

mri_glmfit--y lh.suvr.sm10.mgh --fsgd fsgd.txt --C X.mtx --surf  fsaverage lh --cortex --glmdir lh.suvr

5. Correction for multiple comparisons ( Cluster –wise)

mri_glmfit-sim --glmdir lh.suvr --cache 1.3 neg --cwp  0.05  --2spaces     # Cache 1.3 ( P<0.05)

· In a second analysis for the same set of data, I replaced the first step ( co registration) by the following command line:

spmregister --s name --mov suvr.nii --reg reg.dat --o suvr_T1.mgh

I got the results as attached ( figure1 using bbregister and figure 2 using SPM register)

Kindly,

1. Where this difference came from? In other words, should I expect such like difference between “bbregister” and “spmregister” ?

2. For co registration which command do you recommend  “bbregister” or “spmregister” ?

Best,

Mohamad