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Dear professor John Ashburner, Thank you for your reply and instructions! I think we have these main questions: Is SPM12 able to segment the rat brain tissue after adapting the batch parameters? My impression is that the tissue a priori map in SPM12 is a 6-diamention TPM, and how can we get the TPM for rat? Besides, bet process may be another challenge with SPM12, How can we sucessfully remove the non-brain tissues(muscle,skull...)? SPM5 is indeed too old and is no longer compatible with the MATLAB(version after 2014). I will try to replace the SPM5 files with the method your suggested.Thank you again for your help and look forward to your answer! Respectfully yours, Ying Liu ---------------------------------------------------------------------- Department of Radiology; Zhongnan Hospital of Wuhan University; Wuhan University; Wuchang District, Wuhan City, 430071; Hubei Province, China. At 2019-02-01 23:11:13, "John Ashburner" <[log in to unmask]> wrote: Sorry, but I don't know so much about the spmmouse software. Looking at the contents of the repository, I would guess that you'll need to overwrite some of the existing MATLAB functions of SPM5 with the contents of the "replaced" folder (or put them in a separate folder, which appears earlier in the MATLABPATH). Without reading through the code, I'm not sure where you need to put the various tissue probability maps. If you get an error message, it can be helpful if you let us know a bit more about what it says. SPM5 is now quite old, and we stopped fixing it many years ago. I've just tried it, and it no longer works with the version of MATLAB that I'm using (R2018a). Best regards, -John On Fri, 1 Feb 2019 at 14:14, ÁõÓ± <[log in to unmask]> wrote: Dear professor John, It is really my honor to have reply and instructions from you! In fact i have downloaded the version through the website you just refered to, and also tried to analysis the data. However, together with SPM5, it always fails in the segmentation step. If it is not an error, then it will take a long time until the memory and CPU utilization are maximized or even crashed and finally shut down. I don't know why... Since this link "https://github.com/neurospin/spmmouse" hasn't been updated since 2015, I am worried that the spmmouse software i downloaded is not complete, i wonder wether there is an updated version? Sincerely looking forward to your help and thank you so much! Respectfully yours Ying Liu, PhD student; At 2019-02-01 18:47:12, "John Ashburner" <[log in to unmask]> wrote: Try https://github.com/neurospin/spmmouse . Like many academic packages, it now seems to have moved to GitHub. Best regards, -John On Thu, 31 Jan 2019 at 16:07, Ying Liu <[log in to unmask]> wrote: Hi everybody! I am a fresh postgraduate of Wuhan university (Wuhan, hubei province, China). I have just started my research on rat fmri. I urgently need spmmouse tool now, however, when I enter the website www.wbic.cam.ac.uk/~sjs80/spmmouse.html for downloading, the result is ¡°the page doesnot exsist¡¡±. It's really frustrating. Does anybody has a latest spmmouse toolbox, better for SPM8/SPM12, or SPM5 will also be perfect. Your kind help will mean a lot to me! Thank you all, Ying Liu, PhD student; -- Prof John Ashburner Professor of Imaging Science UCL Institute of Neurology Queen Square Wellcome Trust Centre for Neuroimaging University College London 12 Queen Square, London, WC1N 3BG E: [log in to unmask] T: +44 (0)20 3448 4365 http://www.fil.ion.ucl.ac.uk/ -- Prof John Ashburner Professor of Imaging Science UCL Institute of Neurology Queen Square Wellcome Trust Centre for Neuroimaging University College London 12 Queen Square, London, WC1N 3BG E: [log in to unmask] T: +44 (0)20 3448 4365 http://www.fil.ion.ucl.ac.uk/