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
 

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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
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<Picture 1.jpg>

 
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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
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