Hi Clark/FSL users,
This was very helpful, I followed its instructions, then ran FLIRT, and did not get back what I expected ....
Original data was a 3-D Sagittal MP-RAGE.
Using the instructions from the ToGenerateLASImages doc, I ascertained that the orientation was PIL.
So I ran avwswapdims pilsag z -x -y lassag
then I fired up fslview and the data was oriented exactly like the avg512T1 standard set.
Then I ran this data through FLIRT (using the FSL GUI) with the standard reference.
When I viewed the result with fslview it's orientation was like my original data i.e. in PIL orientation.
Any clues?
TIA
-roddy
Roddy McColl
UT Southwestern
>>> Clark Johnson <[log in to unmask]> 6/21/2007 10:11:31 AM >>>
Agniezka --
-- Using AVWSWAPDIM can be confusing
-- Here's a .pdf that may be useful the next time you need to figure
this out.
http://www.son.washington.edu/informatics/CHDD/UsingAVWSWAPDIM_ToGenerateLASImages.pdf
Clark
Agnieszka Burzynska wrote:
>
> 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
>
>
>
>
>
> ---------------------------------------------------------------------
> ---
> ---
> 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
> <http://www.fmrib.ox.ac.uk/%7Esteve>
> ---------------------------------------------------------------------
> ---
> ---
>
>
>
>
> <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
> <http://www.fmrib.ox.ac.uk/%7Esaad>
> ---------------------------------------------------------------------------
>
>
>
>
>
>
>
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