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FSL  June 2010

FSL June 2010

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Subject:

Re: Should I flip L-R of images from dcm2niigui (MRIcron)?

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

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

Date:

Tue, 15 Jun 2010 14:30:57 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (286 lines)

Hi,

This is very odd but fine.
If you swap things an even number of times then the
determinant is unchanged and there is no left-right
ambiguity in the sense that FLIRT will try to align things
consistently.  However, the labels that you would get in
FSLView would clearly be different for the two different
cases and I can only assume that one is correct!  Are
both the qform_code and sform_code set to non-zero
values?  Whenever the _code is set to zero you can
ignore everything else it says (e.g. qform_code=0 means
the qform information can be ignored).

If the final alignment of the images is fine, and you are
happy with the labelling in FSLView (and for DTI the
vectors also look correct in FSLView) then there is nothing
to worry about.

All the best,
	Mark


On 15 Jun 2010, at 14:15, valeria della_maggiore wrote:

> Hi Mark,
>
> Reading your email on the inconsistencies between qform and sform I  
> got concern about the orientation of our DTI images. We acquired  
> these images on a Phillips scanner and we used r2agui, a matlab  
> script written from someone at John Hopkins, to transform them into  
> nifti format.
>
> the q form is like this
> xorient R to L
> yorient A to P
> z orient S to I
>
> and the sform has the y and z flipped
> xorient R to L
> yorient P to A
> z orient I to S
>
> According to the forum, the bottom one reflects radiological  
> convention. We have not got any warnings and the images viewed in  
> fslview are not flipped in the y and z direction.
> Should we change the q form?
>
> thanks!
>
> v
>
>
> Our DTI images, which we converted using an applet called m
>
> 2010/6/15 Mark Jenkinson <[log in to unmask]>
> Dear Clark,
>
> I am sorry that the FAQ was out of date on this.
> I have just modified the FAQ to adjust it for FSL4.1.
> Basically, it no longer matters whether the storage is
> "neurological" or "radiological" as the FSL tools will
> work correctly with either, or even with a mix of them.
> This did not use to be the case but it is now.
>
> As for your inconsistent qform and sform - THIS IS
> EXTREMELY BAD!  You should convert your images
> again from the original DICOM, as if you have such
> inconsistent information then there is NO WAY of
> knowing which is the correct left or right in the image,
> since the qform information says one thing and the
> sform information says another.  This is why we have
> the warnings.  We also use dcm2nii for our conversions
> but have not noticed this problem.  However, we do not
> use the "reoriented" images.  So check whether the other
> images have consistent information in the qform and sform
> (the sign of the determinant of these matrices needs to be
> the same).  Just running fslorient will tell you what the
> situation is.
>
> With respect to FSLView, it is the case that it tries to display
> the images in a "radiological display" although this doesn't
> have an obvious meaning for images that are differently
> oriented to the standard MNI152.  It is not a problem for
> any of the tools how things are shown in FSLView, as all
> tools will work correctly for any storage type now.  If you
> do wish to see the images in the same orientation as the
> MNI152 template images then you should run the command:
>
>  fslswapdim invol RL PA IS outvol
> and if it gives you the message
>
> Cannot perform requested swap (NERUOLOGICAL/RADIOLOGICAL storage  
> inverted)
> Try the following command instead
> Fslswapdim o_dcm2nii_Output.nii.gz LR PA IS tmp
> then simply do as it says and run the command with LR PA IS instead.
>
> I'm sorry that this is not simpler, but having both qform and sform
> in the nifti standard makes some things complicated.  I am
> intending to overhaul the section relating to this and provide
> a small script that reorients images to match the MNI152
> orientation, as that seems to be what people generally want to do.
> It is not important that this is done - it is simply a preference that
> people have in order to look at their data.  It is only the display
> which is now affected by this - all tools process correctly as long
> as the qform and sform are consistent and correct.  You should
> ideally be able to tell if they are correct by looking at the labels
> that FSLView attaches to the image.  If they are correct and the
> qform and sform are consistent then that is enough for all tools
> to work.  If you also want to see the image in the same orientation
> as the MNI152 then perform the fslswapdim commands as shown
> above.
>
> I hope this helps to clarify things and make things a little less  
> "blackbox".
> Being able to store two different sets of orientation information
> and this being somewhat separate from how they are displayed does
> make it hard to follow, and I've tried to minimise the amount that
> people need to worry about this.
>
> All the best,
>        Mark
>
>
>
>
>
>
>
> On 14 Jun 2010, at 23:53, Clark Johnson wrote:
>
> Mark -- We use dcm2nii for conversion to NIFTI -- As Chunhui Chen  
> mentioned as this thread began -- this program's output includes an  
> image that has been reoriented -- in my case from a SAG acquisition  
> to what appears in FSLVIEW to be Radiologic.
>
> When viewed in FSLVIEW it "looks" like LAS -- the axial image has  
> the left side of the brain on the right side of the image.  But,  
> when you increment the "x" index -- FSLVIEW moves to the right side  
> of the brain.  This seems to suggest that FSLVIEW is presenting in  
> LAS -- but the byte order is actually RAS.
>
> If you request the HDR information for this file (fslhd) you get the  
> error
>
> Inconsistent left-right order stored in sform and qform in file XYZ
> Using sform instead of qform values
>
> And the output attached to this email.
>
>
> In your response on May 5th -- you indicated that FEAT / FLIRT won't  
> have any problem with an RAS oriented image (though possibly we have  
> to turn on "Full search" in FEAT).  However, the "format and  
> orientation conventions" section of the FSL documentation is still  
> pretty unambiguous about this -- stating:
>
> "NIFTI allows the left-right orientation of your data to be  
> specified but we do not recommend using anything but radiologically  
> ordered images with this release."
>
> It is this statement in the documentation that has me confused.   
> FSLVIEW is pretty clever -- but the byte order in the file does not  
> appear to be LAS  -- I am wondering if that means it's not  
> "radiologically ordered".
>
> In a previous response to this issue --
>
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1003&L=FSL&D=0&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=179521
>
> you suggested
>
> "If the labels that you see in FSLView (L, R, A, P, S, I) are in
> the correct places in the image then all you need to do in order
> to reorient your images to axial is:
>  fslswapdim invol RL PA IS outvol
> ..."
>
>
> In an effort to work exclusively with LAS oriented images I've tried  
> the " fslswapdim invol RL PA IS outvol" approach. As noted above,  
> the labels are correct -- I just want the byte order to reflect an  
> LAS orientation as well.
>
> For this file, the suggested fslswapdim call generates several  
> "inconsistent left-right" messages then stops with the following  
> message"
>
> Cannot perform requested swap (NERUOLOGICAL/RADIOLOGICAL storage  
> inverted)
> Try the following command instead
> Fslswapdim o_dcm2nii_Output.nii.gz LR PA IS tmp
>
> Since I think it already is RAS -- this suggested solution does not  
> seem to solve the problem
>
>
> We all love FSL tools -- but sometimes they seem a little like a  
> "blackbox"  -- things are happening and we don't really understand  
> all of the implications.  I am concerned that we are not being  
> careful enough about the L/R orientation of our data and am hoping  
> you can give me some additional guidance
>
> Thank you for all your help.
>
> Clark
>
>
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On  
> Behalf Of Mark Jenkinson
> Sent: Tuesday, May 04, 2010 3:10 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Should I flip L-R of images from dcm2niigui  
> (MRIcron)?
>
> Hi,
>
> I'm not quite sure how you are defining RAS, or similar, for fslview
> *display*.
>
> Anyway, all that *really* matters is that the labels are in the
> correct places on
> the image.  It doesn't really matter which way the image is
> displayed.  All the
> FSL tools should work, regardless of which way the image is stored and
> displayed, as long as the labels are correct.  However, if the
> different images
> are very differently oriented then you should check the registrations
> carefully
> to make sure that they all work correctly.
>
> So, in summary, I wouldn't worry about swapping anything.
>
> As for FreeSurfer problems, you should email the FreeSurfer list about
> that.
>
> All the best,
>        Mark
>
> On 4 May 2010, at 09:11, chen wrote:
>
> Hello FSLers,
>
> I may be asking a stupid question but it really troubled me a while.
>
> I converted dicom files to nift using dcm2niigui (MRIcron). In
> fslview, it displayed in RAS coordinates, but template of FSL are in
> LAS coordinates. Should I filp L-R before doing any further analysis?
> Besides, my structrual imagews were scanned in sagittal view, and
> after  dcm2niigui transforation, it's in PIL coordinates in fslview.
> Should I reorient the image to LAS coordinates too?
> But the letters L R I S A P are labled correctly (at least A-P and I-
> S are correct), which means FSL can read in orientation information
> correctly. So I am confused whetehr I should reorient my data or not?
> I also processed strucutre images with Freesurfer, and the results
> between reoriented and not-reoriented images are different, so which
> one is correct?
>
> Any help is appreciated,
> Thanks!
> --
> Chunhui Chen
>
>
> 网易为中小企业免费提供企业邮箱(自主域名)
> <o_dcm2nii_Output_HD.txt>
>
>
>
>
> -- 
> Valeria Della-Maggiore, Ph. D
> Department of Physiology, School of Medicine
> University of Buenos Aires
> Paraguay 2155, Capital Federal
> Buenos Aires, C1121ABG
> Argentina
> phone 54 11 5 950 9500 (2132)
> http://www.fmed.uba.ar/depto/fisiologia/fdaction.htm
> ------------------------------------------------------------
> being wild and disciplined at the same time....
>

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