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Subject:

Re: orientation in fslview and MNI coordinate system

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Thu, 7 Oct 2004 08:17:37 +0100

Content-Type:

text/plain

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text/plain (97 lines)

Hi,

I didn't realise that you images contain exactly the
same data.  In that case send us a copy of the header
contents (use avwhd) and we can see what the difference
is.

All the best,
        Mark


On 7 Oct 2004, at 02:08, Betty Ann Chodkowski wrote:

> mark,
>
> thank you for your reply.
>
>> The existing fsl release (note that some of this will
>> change in the next release) does not attempt to calculate
>> left-right order anywhere.
>
> okay, good, i understand.
>
> but what i do not understand is why two volumes of the same data with
> the same orientation have different results when registering via FLIRT.
>
> perhaps my belief that these two volumes  have the same orientation is
> incorrect.  perhaps someone might verify or point out my error in my
> attempts to ascertain the orientation of both volumes.  this is what i
> did:
>
> i opened both VolumeA and VolumeB in MEDx as "Raw Generic" after
> defining their volume dimensions.  both volumes have the same
> orientation in MEDx.  is my interpretation of this correct:  since i
> loaded the volumes as "Raw Generic", what i see is what i get, namely,
> they are both of the same orientation *on* *disk*.  when i loaded the
> standard volume into MEDx as "Raw Generic", its orientation is
> different
> from my VolumeA and VolumeB by a 180 degree rotation about the z-axis.
> i thought since i avoided the use of the .hdr file in MEDx that "Raw
> Generic" is WYSIWYG.
>
> perhaps i will try to view both volumes through some other display
> mechanism such as matlab (or imageJ?).  can anyone recommend a viewer
> (for sun solaris and/or mac os x) i might try to verify the orientation
> of the volumes?
>
> thanks, mark, for your clarification.
>
>> Therefore
>> if all of your images are in the same convention then
>> everything is fine - flirt will *never* flip left and right.
>
> okay, this is reassuring.
>
>> Hope that makes things clearer.
>> I'm not sure whether the problem you have with volumeA vs
>> volumeB is about getting the left-right order correct or
>> just about registering images that are 180 degrees
>> different in initial orientation.  Is it the case that
>> your images are 180 degrees different from the standard?
>
> it is the latter case -- my images are 180 degrees different from the
> standard.  i can rotate by doing two avwswapdim y -x z.  but VolumeA
> registers just fine -- a double avwswapdim would cause the registration
> to fail.
>
> but since i believe VolumeA and VolumeB have a the same orientation (as
> determined by loading the volumes using MEDx's "Raw Generic" format), i
> cannot figure out why VolumeA will register to the standard volume
> whereas VolumeB will not.  the resulting html page -- the one with the
> incredibly useful red outline overlay -- shows very clearly that
> VolumeA
> is in the same orientation as standard whereas VolumeB is flipped, ie,
> the subject's nose is pointing in the wrong direction.
>
>> By default flirt only searches +/- 90 degrees from the
>> original orientation, so it is impressive that it actually
>> works for one of the images.
>
> the two volumes are exactly the same data -- just converted from the
> philips scanner format to avw format via two different programs.  i
> will
> check via another display package that both volumes are, in fact, in
> the
> same orientation.  looking at both conversion programs, there is no
> reorientation of the philips data therefore the data on disk is in the
> same orientation.
>
> a bit frustrating.
>
> i am determined to find the difference, though.  i'll let you know when
> i find it.
>
> thanks for your clarifying comments,
> - bettyann

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