Dear Chris Rorden, when I use dcm2nii to convert DICOM images to NIfTI, the output files have three kinds, original nii, o.nii, co.nii. Many people recommend to use co.nii for vbm segment and normalization, but I found some co.nii seemed abnormal, some brain tissue seemed being cropped. Can such co.nii be used for vbm analysis, can you give me some suggestions. Thank you very much

The cropping assumes that you are using a T1 scan that was approximately oriented in the AC-PC plane (anterior commissure, posterior commissure) which is typical for MRI. It looks like your scans are with the angle of rotation more similar to CT scans (where one wants to reduce radiation to the eyes and minimize artifacts from dental fillings). In this case, the dcm2niix cropping function will not work well. I would be especially careful normalizing you r scans to standard space, as the slice angle does not match the template so there may be a poor starting estimate.You may can to try a script like 
  https://github.com/neurolabusc/nii_preprocess/blob/master/nii_setOrigin12.m
For future acquisitions, it may be worthwhile to see if you can have the images acquired to match the MR convention.

Thank you very much! I convert the DICOM to NIfTI by dcm2nii previously, not dcm2niix. And I just tried dcm2niix to convert it, the crop.nii seems no brain tissue were cropped.
1.So I want to ask the if co.nii converted by dcm2nii showed some brain tissue were cropped, is it shouldn't be used for vbm analysis?
2. If crop.nii converted by dcm2niix showed no brain tissue were cropped, can it be used for vbm analysis, since some tools like CAT12 can set orign in the segment preprocess.

I would not use a cropped image if it removes some of the cerebellum. In general, SPM12/CAT12 are very robust for having excess neck in the image, as long as they get a good starting estimate. The origin should be near the anterior commissure. By default MRI scans use the magnet isocenter as the origin. FSL tends to be more sensitive to excess neck as this changes the center of brightness.