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Dear Freesurfer experts,

Could you please let me know how to normalize fMRI data without upsampling the original voxel size from 5 x 5 x 7 mm to 2 x 2 x 2 mm? I have tried this as follows:

1. Register functional (data.nii) to anatomical matrix

bbregister --s $subject --bold --init-fsl --mov data.nii --reg register.dof6.dat

2. Register anatomical to mni152:

mni152reg --s $subject

3. Create registration between functional and mni152

mri_matrix_multiply -im register.dof6.dat -iim reg.mni152.2mm.dat -om reg.mni152.dat

4. Resample func to mni152 space

mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --mov data.nii --reg reg.mni152.dat --o data.mni152.nii --no-resample

I checked the registrations after each step. After step 4, the functional data and the template are not fully aligned if I use “no-resample”. Without no-resample, the registration seems successful, but the fMRI data has a voxel size of 2mm.

Best,

Maria