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Hi Ludovica, here's what you indicate as a necessary first step in the Userguide and I have a few questions about it Before running BIANCA you need to: 1. Choose your base image. This will be your reference space for your input and output images. 2. Perform brain extraction on (at least) one modality to be able to derive a brain mask * 3. Register all the other modalities to your base image for each subject. 1. Does my "base image" need to be a structural image or an MNI is also ok? do you have any specific suggestion? 2. I performed fsl_anat and the command to get a bianca_mask: I have no clarity of idea in relation to whether I have to premask or postmask or both 3. Does a linear registration work fine enough? Thanks, Matteo 2017-07-28 4:57 GMT-04:00 Ludovica Griffanti < [log in to unmask]>: > Dear Matteo, > yes, BIANCA requires some images where the WMH are labelled, to learn how > to classify them in the rest of the subjects. > You will need to prepare some binary images of WMH (1 inside the lesions, > 0 outside) from your data (usually FLAIR is used as the WMH are better > identifiable) > I would suggest 10 subjects to start with (in our experience it works > better if you use the ones with higher WMH load) and then see if you are > happy with the results or you need to add more. > Hope it helps, > Ludovica > > — > Ludovica Griffanti, PhD > Analysis Postdoctoral Research Assistant > Wellcome Centre for Integrative Neuroimaging (WIN) > Oxford Centre for Functional MRI of the Brain (FMRIB) > Nuffield Department of Clinical Neurosciences, University of Oxford > John Radcliffe Hospital > Oxford, OX3 9DU, UK > email: [log in to unmask] > > > > > On 27 Jul 2017, at 7:53 pm, Matteo Respino <[log in to unmask]> > wrote: > > Hi everyone, > > it's the first time I try Bianca and I've been reading the provided user > guide. > I do not get the "training dataset preparation" step: am I supposed to > manually mask the WMH within some of my FLAIR images? > If yes, how many sbj are required for having a training set? > > Thanks in advance > Best > Matteo > > > -- *Matteo Respino, MD* Resident in Psychiatry Visiting Research Fellow in Psychiatry *Clinica Psichiatrica Universitaria* *Facolta' di Medicina e Chirurgia di Genova* Largo Rosanna Benzi, Padiglione 32A Genova, 16100, Italia *Weill Cornell Medicine* 21 Bloomingdale Rd, White Plains, NY 10605