Re: [FSL] Data orientation
Dear Tim,
Thank you for your advice. I applied, but it was still not oriented well. So I tried to figure out how avwswapdim works, namely what x y z means. The rpoblem was to change zxy orientation to be changed into xyz. from what you wrote I deduced that If my old x has to become new y, I have to write y in the place of x (in xyz order), saying: old x will be called now new y.
When I applied different way of thinking: make new x from old z (so I wrote z in place of x in xyz order), it worked.
So instead of
avwswapdim data -y z x data_new
or
avwswapdim data -y z -x data_new,
I did avwswapdim data z –x y data_new.
Does it mean it is a good approach? (I ask before I make mess with bvecs...)
Best wishes,
Aga
On 20.06.2007 22:44 Uhr, "Tim Behrens" <[log in to unmask]> wrote:
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
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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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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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