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Hi Your old x needs to be your new -y your old y needs to be your new z your old z needs to be your new x (or -x, can't tell from this image) hence you will need something like avwswapdim data -y z x data_new or avwswapdim data -y z -x data_new and you will have to change the bvecs to match - the easiest way to do this is to load them into matlab, change them and resave them, but you can do them by hand if you have the patience! T On 20 Jun 2007, at 19:37, Agnieszka Burzynska wrote: > > I thought I flip the data, not the vector data, by using > avwswapdim. I used this command with yzx and somthing indeed > changed, but as I deduce the axis-color connection from fslview i > have now y:blue, z:red, x:green. If I am on the right path at all, > I will try the same with xyz tomorrow morning. What is an elegant > way to flip bvecs? Manually?! > > Sorry for all these primary school questions, but i have to go > through it. > > Best wishes and thanks for any advice, > Aga > > > > On 20.06.2007 19:56 Uhr, "Saad Jbabdi" <[log in to unmask]> wrote: > >> It looks like your v1 vectors are oriented correctly (although you >> still want to look at the vector plot rather than rgb map), the >> colors are different from what you expect because fslview >> considers blue as being z direction, and not top-down. this is why >> the corpus callosum is blue on your bottom left image, the >> callosal fibres are in z direction. (same for red and green). You >> cannot simply flip the vector image, as you would need to flip the >> vectors (interchange the coordinates). To avoid confusion, it is >> preferable to flip the data (and the bvecs), and run dtifit again >> with conventional brain orientation (axial slice on the bottom >> left!). >> >> cheers, >> saad >> >> >> On 20 Jun 2007, at 17:36, Agnieszka Burzynska wrote: >> >>> >>> >>> Here it it. Instead of x y z axes I have z x y axes, and as a >>> result I get >>> blue, red, green, instead of red, green, blue.... >>> >>> Thank you, >>> Aga >>> >>> >>> >>> On 20.06.2007 17:03 Uhr, "Tim Behrens" <[log in to unmask]> >>> wrote: >>> >>> >>>> Can you put a snapshot of the colour coding on the web, or send >>>> it in? >>>> >>>> Cheers >>>> >>>> T >>>> On 20 Jun 2007, at 14:58, Agnieszka Burzynska wrote: >>>> >>>> >>>>> Dear all, >>>>> After running DTIFit, when I overlay FA maps and V1 I see in all >>>>> subejcts >>>>> but one the correct color-coding of diffusion direction. It >>>>> seems that >>>>> something happend already before data conversion. I treid >>>>> avwswapdim, but so >>>>> far was unscuccessful. >>>>> >>>>> Can anyone tell me how could this happen with just one scan and >>>>> what to do? >>>>> >>>>> Best wishes, >>>>> Aga >>>>> >>>>> On 20.06.2007 15:24 Uhr, "Steve Smith" <[log in to unmask]> >>>>> wrote: >>>>> >>>>> >>>>>> Hi, >>>>>> >>>>>> Sure - just type "cluster" to get the usage, and output the >>>>>> cluster >>>>>> size image for use in the thresholding. Then you can use >>>>>> avwmaths++ >>>>>> and avwstats++ to get further stats using these masks. >>>>>> >>>>>> Cheers, Steve. >>>>>> >>>>>> >>>>>> On 19 Jun 2007, at 17:54, Ping-Hong Yeh wrote: >>>>>> >>>>>> >>>>>>> Dear FSLers, >>>>>>> >>>>>>> Is there a way to use cluster command on randomise t-maps for >>>>>>> thresholding >>>>>>> the minimum cluster size, and then output the mean and standard >>>>>>> deviation >>>>>>> of each subject and individual group for each cluster? >>>>>>> >>>>>>> Thanks. >>>>>>> >>>>>>> Ping-Hong Yeh >>>>>>> >>>>>> >>>>>> >>>>>> ----------------------------------------------------------------- >>>>>> ---- >>>>>> --- >>>>>> --- >>>>>> 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 >>>>>> ----------------------------------------------------------------- >>>>>> ---- >>>>>> --- >>>>>> --- >>>>>> >>> >>> <Picture 1.jpg> >> >> >> --------------------------------------------------------------------- >> ------ >> Saad Jbabdi, >> Postdoctoral Research Assistant, >> Oxford University FMRIB Centre >> >> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >> +44 (0) 1865 222545 (fax 222717) >> [log in to unmask] http://www.fmrib.ox.ac.uk/~saad >> --------------------------------------------------------------------- >> ------ >> >> >> >> >> >> >