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
>
>
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