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I have a question regarding the re-orientation of a lesion mask created in MRIcro. 1) I have created a lesion mask in MRIcro from a high-resolution T1. (exported as smoothed Analyze image) 2) I changed the orientation of the T1 from the display window in SPM2. (slight pitch (.2 radians) and set origin to the AC) The lesion mask and T1 now have different orientations. Should I apply the same origin and rotations to the lesion mask? I tried this and the normalization routine failed, saying the images were not in the same orientation. Any help is appreciated, karl Neggers, S.F.W. (Bas) wrote: >We used Matthew Brett's method, as published in NeuroImage: > >Brett M, Leff AP, Rorden C, Ashburner J. Spatial normalization of brain images with focal lesions using cost function masking. Neuroimage. 2001 Aug;14(2):486-500. > >http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11467921 > >It worked well for us, the papers are submitted at present. We didn't do VBM, but instead calculated lesion overlap ratios. I'm not sure with respect to VBM if this is what you want. > >Good luck, > >Bas > >-----Oorspronkelijk bericht----- >Van: SPM (Statistical Parametric Mapping) >[mailto:[log in to unmask]]Namens Yong Zhang >Verzonden: woensdag 26 januari 2005 21:46 >Aan: [log in to unmask] >Onderwerp: [SPM] Spatial normalization with the existence of brain >lesion > > >Dear SPMers: > >Currently I am working on a VBM project comparing >childhood brain tumor survivors with normal >controls. The lesion region resulting from resection >caused distortion during spatial normalization. >To solve this problem, one methos is to use >affine registration only and the other is to mask >out the lesion region. I am wondering if there >is any other solution for this problem. I >searched the SPM achives, but very few >documents were found for this issue. >Where can I find more sources for this problem? >Thanks a lot! > >Yong > >