Dear all,

Recently i'm using both MRIcron do the tumor segmentation.

For each patient we have 2 scans: coronal and sagittal.

I found that when i draw the tumor with MRIcron on the coronal scan, the segmentation(ROI) can be used on sagittal scan (only in MRIcron, the ROI from coronal scan cover the tumor area that shown in sagittal scan)
'''
In MRICron,
when load coronalImage as main image, load coronalROI as overlap image, the ROI cover the tumor area.
when load sagittalImage as main image, load coronalROI as overlap image, the ROI still cover the tumor area well.
'''

But when i try to extract tumor feature with ITK or other tools,
featureExtraction(coronalImage,coronalROI); it work ;
featureExtraction(sagittalImage,coronalROI); error shown up.
error message said that the ROI matrix shape is different from the Image matrix shape.

I'm wondering how MRIcorn do the overlapping process, especially between 2 images with different shape.

Thank you for your help, best regards.
Ningrong

Ps. I attached the a patient's coronalImage, coronalROI, and sagittalImage in the attachment.

Your coronal image has the resolution 208x11x320 voxels (in L/RxP/AxI/S dimensions), in contrast your sagittal scan is 9x224x324 voxels. Many tools require drawing masks to have a perfect one-to-one correspondence with the image they belong to. In contrast, my tools interpolate an image if it does match perfectly. Therefore, this is a limitation of the other tools you are using. 

If you use SPM, you can use the "coreg" function to warp estimate the transform from the coronal image to your sagittal image, and then apply this function to your segmented mask. 

If you use FSL's FLIRT, choose your segmented mask as the "Secondary image"

Thank you Chris!
I will try those tools.
I'm just wondering how mricron do it without warp.
The result look perfect, i can impliment same method in other software.
Thank you
Ningrong