I am assuming all images are Nifti format given you are using ITK snap. Also I'm assuming your images are colocalized (subject was not re-registered/moved or sequences are different due to distortion such as EPI sequences).

This requires some coding for example in Matlab:

1. Read in your New MRI Vol_Info = niftiinfo('C:/path/to/original/MRI_Volume')

2. Check the matrix size for Number of rows,columns and planes.

2. Read in your segmentation Mask = niftiread('C:/path/to/segmentation')

3. Reslice your segmentation New Vol = imresize3(Mask,[numrows numcols numplanes])

4. Save your new segmentation niftiwrite(Mask, 'C:/path/to/new/MRI_Segmentation')

If you need to you can also zero pad your segmentation Mask to make it the right size if the field of view is different (https://uk.mathworks.com/help/images/ref/padarray.html).

The above steps can also be done in FSL/Python etc.

Good luck!

thanks a lot! I´ll try it for matlab.

Otherwise, there is any way to do it directly in ITKsnap or another segmentation program (Osyrix, Horos, 3DSlicer)?