Hi,
I'm glad that helped.
If you are confident that your labels are correct then you
can continue to use the same commands as before. Neither
fslswapdim nor fslorient have changed significantly for some
time. FSL always interprets the images in the same way that
FSLView shows them. So as long as FSLView is fine (and
hence the reason I keep talking about checking the labels)
then everything inside FSL will be fine.
All the best,
Mark
On 19 Nov 2010, at 21:00, Woodman, Sandra wrote:
> Mark,
>
> Thanks for your thorough response! It has been a bit confusing, but this has
> helped clarify.
>
> One additional question.. currently we are working in a freesurfer environment,
> which doesn't recognize fslreorient2std as a command. In this case is it okay
> if we continue with our current protocol, ie using fslswapdim and fslorient? We
> have looked over some of our old data (images with hemispheric adnormalities) in
> fslview against tkmedit (freesurfer viewer) where we know the orientation is
> correct and it appears that all our images are in correct orientation with the
> correct labels (L/R). Has there been any changes in FSL recently (past year)
> that would have effected the way FSL unpacks and orients, ie does FSL
> automatically swap/reorient images at any stage?
>
> Thank you for your help!
>
> Sandra
>
>
>
> Sandra Woodman
> Mood and Motor Control Laboratory
> Athinoula Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 120 6th St.
> Charlestown, MA 02129
> Tel: 617-643-6245
> Fax: 617-726-1351
> Email: [log in to unmask]
>
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Mark Jenkinson
> Sent: Fri 11/19/2010 5:21 AM
> To: [log in to unmask]
> Subject: Re: [FSL] FSL orientation/swap query
>
> Dear Sandra,
>
> Once upon a time the nifti fairy gave us a new data format.
> Unlike the nasty old Analyze format, this new format allowed
> us to store information about orientation in the image itself
> and so the analysis programs no longer had to guess which
> way around the images were stored (or, as was more common,
> assume a given default and let the users make sure that their
> images adhered to that ordering).
>
> So this was the situation in 2004 when FSL 3.2beta was
> released. We put in nifti support, but although most of our
> tools could cope with different orientations, not 100% of
> them were able to do this, so we stuck with the convention
> that people needed to make sure that their images adhered
> to the "old" style FSL convention - which was to be "like" the
> MNI152 template images. By "like" we mean that you could
> rotate your image to make it match this template (that is,
> no reflections were needed). This is related to left-right
> ordering but a little more complicated. I decided (in one
> of the worst decisions I've ever made in FSL) to call this
> convention "radiological ordering". This terminology, and
> the intrinsic complicated nature of storage vs voxel coordinates
> vs "world" coordinates, has caused a lot of confusion. However,
> this was a *temporary* situation (that is, requiring things be
> stored in the "old" FSL convention) and was resolved fully in
> the FSL4.0 (2007). Unfortunately, the belief that FSL *needed*
> things in the old convention (radiologically-ordered) persisted
> well past the point that this was actually true. It has been
> happy for quite a long time now with data in *any* ordering.
> So there is *no* need to convert anything between different
> orderings (i.e. between "radiological" and "neurological").
>
> As I said though, people still wanted to swap between these
> and so fslswapdim and fslorient were regularly used and
> these are *dangerous* operations as it is really very, very
> easy to get the left and right parts of the images mislabeled
> as a result of using these tools incorrectly. Partly to help
> avoid these problems I introduced a label-based syntax
> for fslswapdim a while ago, and more recently have introduced
> a new tool, fslreorient2std. This new tool is there for a different
> reason - not to convert between orderings ("radiological" and
> "neurological") but, instead, to reorient the image so that it
> appears, in FSLView, with the same slicings as the standard
> template brains (MNI152). This therefore changes the
> *orientation* but not the *ordering*. It seems that a lot of
> people confuse these two issues, and a lot of people are
> unhappy if their images are not in the same orientation as
> the MNI152 template images. However, for the analysis
> it doesn't matter if they are in the same orientation or not,
> which is why we'd never worried about it much in the past.
> It is purely an issue of display (although there can be minor
> benefits in the registration).
>
> The other important issue to bring up here is labels in FSLView.
> These are *THE MOST IMPORTANT* aspect of data orientation
> and need to be checked. It is absolutely crucial that these
> labels are correct (as seen in FSLView) when you look at your data.
> If the labels are not correct then *DO NOT* do any processing until
> they are fixed. To fix these labels, if they are incorrect, requires the
> use of fslswapdim and fslorient, and this is really one of the few
> instances where people need to interact with these tools. If the
> labels are fine, then I *strongly* advise people not to use fslswapdim
> or fslorient. In the early days of nifti it was quite common that images
> were incorrectly labeled when they were converted to the nifti format
> from their native scanner format, but these days it is rare. However,
> be vigilant and always check the labels. Obviously it is extremely
> difficult/impossible to tell left from right in the brain by visual inspection
> (at least for most healthy brains) and so it is a *really good idea* to
> attach something like a vitamin/oil capsule to the subject when
> scanning so that you can tell left from right in the actual MR images.
>
> As different centres have different scanners, protocols, conversion
> routines and so forth, we cannot recommend a general workflow
> beyond inspecting your data and fixing problems if they arise.
> If there is no *problem* with the labels, but you just want your
> images to look like the MNI152 images, in terms of orientation,
> then use fslreorient2std. There is no need in FSL (and hasn't
> been for some time) to convert anything between "radiological"
> and "neurological" ordering. Just forget about this in the way
> that you can forget about the datatype that the image is stored
> in. It is a technical detail and is currently dealt with fine within
> the software. The only instance I can imagine that it might
> play a role is when you are using data across several different
> packages and some of them are not fully compliant with
> both orderings (as the very old versions of FSL used to be).
>
> There is more information on the tools and some technical
> details about orientations and orderings on the webpage
> for FSLUTILS. Look at the "Orientation-related Utilities"
> section of: http://www.fmrib.ox.ac.uk/fsl/avwutils/index.html
>
> I really strongly recommend that people do not use fslswapdim
> or fslorient unless they absolutely have to because their
> labels are *incorrect*. I know I said this above, but I would
> really like to emphasize this point, as I've seen far too much
> incorrect, and unnecessary, use of these tools causing problems.
>
> If you are worried about old data then just *check the labels*
> in FSLView. As long as these are correct then everything is fine.
> The labels are the only crucial thing. Then, if you like, you can
> apply fslreorient2std to put the images in the same orientation
> as the MNI152 brains, but this is not necessary, it is only if that
> is what you like to see in the viewer. It will not affect the analysis.
> Once again, it is *only the labels* which are important. OK, I
> think I've probably emphasized that enough now.
>
> I hope this has answered all your questions. It is a pity that
> there is so much confusion about these issues, and I hope
> that this has helped.
>
> All the best,
> Mark
>
>
> On 18 Nov 2010, at 22:34, Woodman, Sandra wrote:
>
>> Hi,
>>
>> We recently spoke with someone doing fMRI analysis with FSL and they ran
>> into some issues with finding that using fslswapdim and fslorient was
>> actually flipping their data such that right was left and left was right
>> (the functional header said it was in neurologic orientation and the
>> structural said radiologic; when he swapped only the functional images,
>> the functional and structural became mirror images of each other). I
>> believe he heard from someone on the FSL list who mentioned that the
>> procedures for dealing with orientation have changed recently, and that he
>> no longer needs to use fslswapdim (and maybe fslorient, too?).
>>
>> So here are our questions: Was there really a change in how orientation
>> is dealt with, and if so, does it affect all types of images (fMRI,
>> structural, DTI, etc.)? Do we need to still run fslorient or is it just
>> fslswap that should not be used? If orientation procedures have indeed
>> changed, when did this change take effect? And finally, at what stage do
>> the changes apply, i.e. was there a change at the stage of unpacking or
>> is the change further downstream (I'm asking this because we did some
>> recent processing of images that were unpacked awhile ago, so they may
>> not be affected by this change and would still need to be swapped--I
>> think).
>>
>> Our current questions are specifically about DTI analysis, but we will
>> also be using FSL for fMRI in the near future. We are currently using both
>> bedpostx/probtrackx and randomise for the DTI analyses. Also, we are using
>> unpacksdcmdir to unpack our images. We are using NIFTI format images.
>>
>> Thank you!
>>
>> Sandra Woodman
>>
>>
>>
>>
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