Dear all,

I am a beginners for the brain image analysis. Recently, I have some problems when using the dicom2nii.exe:

1. I am going to using the freesurfer to segment the hippo. Each of the T1 Dicom images has many frames, so I try to use the dicom2nii.exe to convert the dicom-format to nifti-format. I got three types of the output: 'o***.nii', 'co***.nii', '***.nii'. I know that the 'o' is stand for reorient and 'c' is for the crop. But I am a little confused that which one would be better for the further analysis in freesurfer and why ?

2. Due to I am not familiar with the code, could any one tell me the specific steps during the cropping ? Is the cropping carried based on the template or only cut the non-brain tissues ? The cropped output sizes of the different subjects are different, so perhaps it is cropped by cutting the non-brain tissues, right?