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Dear Jeff, I'm having a lot of trouble reading your open office format. Could you please resend as plain text. All the best, Mark On 16 May 2006, at 20:09, Jeffrey Spielberg wrote: > Hi, we are also having this problem after using bet. I am attaching a > document with the details for our system that you asked Matt for, in > the hope that this can help you track down the problem, thanks, > Jeff > > On 5/15/06, Mark Jenkinson <[log in to unmask]> wrote: >> Dear Matt, >> >> I cannot replicate this problem at our end with any combination >> of Analyze or Nifti. >> >> Could you please let me know the following details: >> - your platform >> - the version of FSL you are using >> - the avwhd output of the input and output images >> - the exact commands that you are running >> >> Hopefully this will let us track it down. >> All the best, >> Mark >> >> >> >> On 15 May 2006, at 19:31, Matt Holloway wrote: >> >> > Hi, >> > >> > I'm trying to brain extract and noise-reduce a set of T1 structural >> > images >> > to get these images ready for VBM analysis in SPM2. While the >> > process of >> > Brain extracting and SUSAN are going smoothly, and nicely brain- >> > extracted >> > and de-noised images are being produced, I can't figure where the >> > coordinate >> > system is getting modified. Immediately following Brain-Extraction >> > the "mm" >> > values in FSLview on the X, Y, and Z planes are changing from the >> > original >> > ~-90mm to +90mm on say the X-axis, to something like 21090mm to >> > 21170mm. >> > >> > I believe this modification of the raw-coordinates may be playing >> > into so >> > difficulties making a custom t1-template from these images down the >> > road. >> > I'm also seeing some changes in the header files evident by using >> > avwinfo, >> > in terms of the size of each dimension. >> > >> > Any insight you could offer would be wonderful. >> > >> > Thank you >> >> <bet_details>