Preprocessing with brain-lesioned patients

Hello all,

I would like to know whether some of you have a good preproc pipeline to deal with large brain lesions in fMRI?
I work on a patient with large bilateral and symetric lesions, secondary to a PRES, with enlarged ventricles, and sequels on his white matter.
Different strategies I have heard of are
1/ brain voyager, but which is paying;
2/ MIPAV, but i can’t understand how to deal with my altered brain, since there is not so many tutos…;
3/ I have tried to make a mask of my lesion, and then to substract it from my anat volume, then segmenting and normalizing my anat_minus_lesion scan (0 value in voxels included in the lesion), using CAT12, but an error occurs systematically (maybe the lesion voxels value should be different from 0?);
4/ working in the native space since it is for now a single case study, which is ok, but I have to analyse resting state and DTI for this same patient, and we will want to compare him to other healthy subjects, or to overlay some atlases to make some analyses, so I think I won’t be able to keep on working in his native space…

So if someone has a good tutorial for this kind of preprocessing (actually just for the normalization part), or knows how to deal with MIPAV, which I have been told was great, let me know!

Thanks for your time,


Hello Fabien

Have you considered fMRIPrep?



No, I have never heard of fMRIPrep, will give it a look.
If possible I would prefer to stay stuck on SPM, but if no other choice, i will try it!