There is a parameter in dcm2nii to control when to re-orient the nifti image
once it is converted from dicom files.
On Mac/Linux, there is a file named dcm2nii.ini under ~/.dcm2nii (hidden
folder). On Windows, the file is called dcm2niigui.ini in the MRIcroN folder
of your installation.
You can change the value of MinReorientMatrix to force dcm2nii to reorient
(or not) for any images, depending on the matrix size of the image. Any
image with acquisition matrix larger than the value will get re-oriented.
On Wed, 18 Mar 2009 22:56:32 +0800, Chun Meng <[log in to unmask]> wrote:
>It is quite interesting to know more about dicom2nifti. And I just
>encountered a strange problem, too.
>For 3d images, the output from dcm2nii generally includes 3 files:
>t1*.nii.gz, ot1*.nii.gz, cot1*.nii.gz. ot1* is from reorienting t1* and
>cot1* just gets some neck-clip. But on one subject of my data, the output
>has only t1*.
>I suspect that some information writtern in dicom files of this subject is
>abnormal, which leads to the change of dcm2nii result. Although I could
>reorient it by hand, I am still puzzled where it breaks down.
>Thanks for any suggestion!
>2009/3/18 Mark Jenkinson <[log in to unmask]>
>> Development sequences are tricky in this way.
>> It really matters what information gets written into the dicom files.
>> Glad you found a solution.
>> All the best,