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Mark, I can certainly wait until early next week and am overjoyed that your group is working on it!! Sincerely, Marc On 1/11/08, Mark Jenkinson <[log in to unmask]> wrote: > > Dear Marc, > > Thanks for the files. > I have figured out what the problem is. The reason is related to the > image resolution, as you guessed. We currently do not compensate > for large changes in voxel volume in tbss_deproject in the same way > that flirt compensates in the affine case. Consequently, it is easy for > voxels in the 1mm^3 space to get missed out when doing the > deprojection (as it only looks at one coordinate per voxel in the > original space). > > We will work on a solution to this problem and get back to you > soon. A temporary solution is to backup your image containing > the blobs of interest and substantially dilate those in the original > file prior to running tbss_deproject. Using a 3x3x7 kernel did the > trick for me when I tried it. You can do this with fslcreatehd and > fslmaths. However, we should have a better solution early next > week if you can wait. > > All the best, > Mark > > > > On 2 Jan 2008, at 20:13, Marc J. Dubin wrote: > > > Mark, > > > > Thanks, This still is not resolved. I will upload the tarred images > > in the > > next 1-2 days. > > > > I really appreciate your help with this!! > > > > Marc > > > > On 1/2/08, Mark Jenkinson <[log in to unmask] > wrote:Hi, > > > > Is this resolved? > > I doubt it is an issue of resolution, as you should get non-zero > > partial volume still. Also, if it works for some of these images > > at this resolution, then it should work for all. > > > > If you are still having problems with this, please upload a tarred > > set of images for one of the offending subjects and we'll have > > a look. > > > > All the best, > > Mark > > > > > > On 22 Dec 2007, at 13:03, Marc J. Dubin wrote: > > > > > I am using the default, which I believe is trilinear.... > > > > > > Could it have something to do with the resolution of the > > > native space images, which is 1.7x1.7x5mm? > > > > > > Best, > > > Marc > > > > > > On 12/22/07, Steve Smith <[log in to unmask] > wrote:Hi, this is > > > probably because you are using the -n interpolation option. > > > Have you tried without this option? > > > > > > Cheers, Steve > > > > > ---------------------------------------------------------------------- > > > -- > > > Stephen M. Smith, Professor of Biomedical Engineering > > > Associate Director, Oxford University FMRIB Centre > > > > > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > > > +44 (0) 1865 222726 (fax 222717) > > > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > > > > > ---------------------------------------------------------------------- > > > -- > > > > > > On 21 Dec 2007, at 05:34, Marc Dubin <[log in to unmask]> wrote: > > > > > > > Dear FSL Users, > > > > > > > > I am using TBSS_deproject 3 to invert the TBSS from MNI space > > back > > > > to native space. > > > > I create grot file from a 45 pixel blob in a tract of interest in > > > > MNI152. TBSS_deproject 3 > > > > then runs without errors and looking at the native space images, I > > > > am able to find the > > > > inverted blob for most subjects, but there are several subjects in > > > > which the blob is nowhere to > > > > be found and in fact running fslstats on these native space images > > > > reveals that in fact there > > > > are no nonzero voxels. > > > > > > > > Any suggestions on what might be going on with these subjects > > would > > > > be greatly appeciated. > > > > > > > > Sincerely, > > > > Marc > > > > > > > > > > > > > > > > -- > > > Marc Dubin, MD PhD > > > Resident in Psychiatry - PGY4 > > > Weill Cornell Medical College > > > > > > 212-746-3764 (work), 646-831-8886 (cell) > > > > > > > > -- > > Marc Dubin, MD PhD > > Resident in Psychiatry - PGY4 > > Weill Cornell Medical College > > > > 212-746-3764 (work), 646-831-8886 (cell) > -- Marc Dubin, MD PhD Resident in Psychiatry - PGY4 Weill Cornell Medical College 212-746-3764 (work), 646-831-8886 (cell)