I have run FreeSurfer 5.3 recon-all, getting different stats output, for these cases of anatomy input: (1) mprage DICOM series converted with dcm2nii (2) fslreorient2std (RL PA IS) on the dcm2nii output (3) mprage DICOM series converted with mri_convert
Differing example results include these from lh.BA.stats: case 1: BA1 1115 583 2017 2.511 0.650 0.175 0.155 66 9.1 BA2 3686 2392 5986 2.342 0.615 0.123 0.047 44 7.2
case 2: BA1 1043 585 2060 2.569 0.637 0.181 0.226 169 4.8 BA2 3569 2357 6064 2.397 0.612 0.123 0.050 38 5.9
case 3: BA1 1071 558 1994 2.583 0.617 0.159 0.181 66 6.5 BA2 3654 2364 6191 2.461 0.631 0.121 0.058 42 6.9
Is this as expected? Are there any options that I should apply to indicate that the orientation is RL PA IS if I use the same anatomy.nii.gz file in case #2 as prepared for FSL? Or must I always either use mri_convert to generate the input for recon-all? Or is there a command I should be running first to reset my RL PA IS image to a particular orientation required by recon-all?
Thanks,
Kathy Pearson