Well, I tried to avoid FSL, and used only Freesurfer tool to do the same
thing. I found there was the same issue when an image with 32-bit float
point data type converts to 32-bit integer. No problem for the convertion
from 32-bit float point to 8-bit unsigned integer.
Wayne
On 05/10/10 10:44 AM, "Wayne Su" <w...@interchange.ubc.ca> wrote:
> 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 0¹ value is changed to
> 2.1e+09¹, 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
>
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