Hello everybody!

I am quite new to bioimaging suite and want to use it to fuse/coregister CT images to MRI images. This seems to work perfect, since the results show up nicely coregistered *within* bioimaging suite. If I save the coregistered Nifti file, close bioimaging suite and load it up again, it remains nicely coregistered.

However, when I open the nifti files e.g. in SPM or any other viewer, the pictures are not coregistered at all (e.g. by using the check reg function of SPM).
Does anyone have a clue why this is the case? I always had thought that nifti file formats are quite interchangeable across software suites?

Any suggestion is very welcome!

Thanks in advance, yours, Andy

Andreas,

This is an "origin" issue. Bioimage Suite does not trust (ignores) the origin flag in an image whereas SPM does not, so your original nifti images have slightly different meanings in each software (plus BioImage convertes everything to its standard orientation "on Load" and stays there). Try saving your reference image out from BioImage Suite and see if SPM likes this.

Xenios

Hi Xenophon,

thanks a lot for your suggestion, this would make complete sense. However, if I save the reference, SPM still doesn't "like" it.
Probably the origin issue is not resolved by this, right?
Any other suggestions?

Thanks, yours, Andy

I would copy the image in spm and replace the image matrix (i.e. the actual intensities) of the reference with the resliced image and see if this helps.