center way out of the origin of the world coordinate system

[Run Jin]

Hi All,

I have encounter a problem when running the t1-freesurfer pipeline. It shows that there are 25 files have a center way out of the origin of the world coordinate system. It also suggests a command using the iotools to recenter the above 25 images. I was wondering what does this notification mean? Please see below photo.

Then, I ran the suggested command and successfully re-ran the t1-freesurfer pipeline. There was no more errors or warnings and I got the outputs. Is this a correct way to solve this issue? Do I need to do anything else?  

Thank you for your kind attention and help!

Best,

Rachel

[Rachel Run Jin]

To follow up, I've found the explanation of this operation in the Clinica's 2021 paper:

center-nifti: This command takes a BIDS directory as input and outputs the same BIDS with centered NifTI: the NifTI headers are modified to set the origin of the coordinate system at the center of the image. This correction is crucial for SPM which is especially sensitive to NifTI files whose origin does not correspond to the center of the image.

However, I'm still unclear about what this step is actually doing. Can anyone help to clarify it? Thank you very much.

Rachel

[Nicolas Gensollen]

Hi Rachel,

You did right by running the "center-nifti" utility before running the T1Freesurfer pipeline even though it is mainly to prevent issues with SPM, which may occur with the PETSurface pipeline that can eventually be run after T1Freesurfer.

Even if you're not planning to run PETSurface, it will not hurt you to center your images before running T1Freesurfer.

You can find more information about what this centering utility is doing on its documentation page: https://aramislab.paris.inria.fr/clinica/docs/public/dev/IO/#center-nifti-center-nifti-files-of-a-bids-directory

Hope this helps!

Best,

Nicolas

[Rachel Run Jin]

Hi Nicolas,

Thank you so much for your prompt response and clear answer! I was on leave for the last two weeks, so my response is delayed.

Yes, I have checked the documentation page introducing the details of this function and have no more concerns.

Cheers,
Rachel