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Thank you once again! I think that I have run the GLM correctly. I have one more quick question. Is there a link or discussion that discusses the statistical analysis of the FSL-VBM data once I have run it through the final step? I know there are some very useful guides on the tutorial page, but I don't think I am aware of the proper systemic way to approach this step or the files that I need to be paying attention to (and commands) Thanks again! On 3/8/12 10:36 AM, "Gwenaëlle DOUAUD" <[log in to unmask]> wrote: Hi Matthew, no worries. In the GLM wizard that you used for (presumably) the unpaired t-test with two groups, you just need to give the overall number of subjects in your study and the right number of subjects for your first group, i.e. HV here... You can always check with any kind of text editor if your design.mat seems right. Cheers, Gwenaëlle -------------------------------------------------------------------- Gwenaëlle Douaud, PhD FMRIB Centre, University of Oxford John Radcliffe Hospital, Headington OX3 9DU Oxford UK Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717 www.fmrib.ox.ac.uk/~douaud -------------------------------------------------------------------- ________________________________ De : "Benage, Matthew (NIH/NINDS) [F]" <[log in to unmask]> À : [log in to unmask] Envoyé le : Jeudi 8 mars 2012 15h29 Objet : Re: [FSL] Re : [FSL] FSL-VBM Thank you for the insightful message! That is very helpful. I don't mean to be a pest, but I am not certain how to properly adjust my design.mat. I created the design matrix with glm, but I don't know how which way of adjusting the design.mat is appropriate. Sorry this is my first time! On 3/8/12 9:52 AM, "Gwenaëlle DOUAUD" <[log in to unmask]> wrote: Hi Matthew, when you say you've organised your directory, do you mean that you have put the prefix HV to all your controls' images and TS for all your patients'? If so, then yes, the first images of the final GM_mod_merg will be of the HV group, then the TS group (and you need to adjust your design.mat accordingly). Cheers, Gwenaëlle -------------------------------------------------------------------- Gwenaëlle Douaud, PhD FMRIB Centre, University of Oxford John Radcliffe Hospital, Headington OX3 9DU Oxford UK Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717 www.fmrib.ox.ac.uk/~douaud -------------------------------------------------------------------- ________________________________ De : "Benage, Matthew (NIH/NINDS) [F]" <[log in to unmask]> À : [log in to unmask] Envoyé le : Mercredi 7 mars 2012 22h08 Objet : [FSL] FSL-VBM Hello, I really appreciate the great work that you have put into creating a software like FSL. I just have a quick, easy question. I used the GLM wizard for creating the proper design matrix for my statistics. I want to make sure that the group designations are as I think they are. I organized my directory into HV (healthy volunteer) and TS (tourette's syndrome). In the directory it read the files in alphabetical order. Am I justified in concluding that the A group is the HV cohort and the TS cohort is the B group? Thanks