Hello Freesurfer Users,

I am feeling very bad when I am using mri_convert. There are two problems:

1. When I converted a file in mgz  format to nii.gz format, and did some volume calculation (mask and addition) by using fslmaths from FSL, then converted back to mgz.  If the image type is uchar, it works fine. If the image type is int, the intensities changed. The ‘0’ value is changed to ‘–2.1e+09’, others also in very large number (look like read the data from wrong place).  Here is the code I used:
   

        ${FREESURFER_HOME}/bin/mri_convert aparc+aseg.mgz aparc+aseg.nii.gz -odt int
        ${FSLDIR}/bin/fslmaths aparc+aseg -mas right_vect_mask_inv -add right_vect_mask aparc+aseg
        ${FREESURFER_HOME}/bin/mri_convert aparc+aseg.nii.gz aparc+aseg.mgz -odt int

        If no fslmaths calculation, convert back to mgz right way, no problem found.

2. when the –conform is used, some head were rotated a little bit, but not for others. I am wondering how to avoid the rotation?

Regards,
Wayne