Compatibility of image formats - Slicer and FreeSurfer

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Compatibility of image formats - Slicer and FreeSurfer

azaitsev
Hello:

I think this message has to be addressed to both Slicer and FreeSurfer
forums, but I start from this Forum.

We need to combine Slicer and FreeSurfer modules, so (command line)
conversion from mgz to NIFTI format and back is the must.
The problem is that after "mgz-nii" conversion the image origin is being
changed (as seen from Slicer GUI), and the mystery is that reverse
conversion restores the orientation.

How to reproduce:
mri_convert T1.mgz T1.nii
mri_convert T1.nii T1_restored.mgz

The T1.mgz and T1_restored.mgz will have the same origin, while T1.nii
will have another origin (see attachment).

Using reslice like (-rl) option does not help.
Registration is not a universal option.

Thank you,

Alex


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Picture_mgz2nii.png (151K) Download Attachment
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Re: Compatibility of image formats - Slicer and FreeSurfer

Aucoin, Nicole
Hello,

If you can verify that this isn't an mri_convert issue, the Slicer
community can help.
As a double check, what happens if you open up Slicer, load the T1.mgz,
then in the Save widget, select NIFTI as the output format, then reload
T1.nii?

Nicole

azaitsev wrote:

> Hello:
>
> I think this message has to be addressed to both Slicer and FreeSurfer
> forums, but I start from this Forum.
>
> We need to combine Slicer and FreeSurfer modules, so (command line)
> conversion from mgz to NIFTI format and back is the must.
> The problem is that after "mgz-nii" conversion the image origin is being
> changed (as seen from Slicer GUI), and the mystery is that reverse
> conversion restores the orientation.
>
> How to reproduce:
> mri_convert T1.mgz T1.nii
> mri_convert T1.nii T1_restored.mgz
>
> The T1.mgz and T1_restored.mgz will have the same origin, while T1.nii
> will have another origin (see attachment).
>
> Using reslice like (-rl) option does not help.
> Registration is not a universal option.
>
> Thank you,
>
> Alex
>
>  
>
> ------------------------------------------------------------------------
>
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>
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> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject

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