> Sorry to bring up orientation issues again, but I want to be 100% certain
> that when we view our results, right is right and left is left.
>
> I use Freesurfer's mri_convert to convert the DICOM images (from GE 3T) to
> Analyze format (e.g. image001.{img,hdr,mat}, ..., imageXXX.{img,hdr,mat}).
> Doug Greve from NMR has assured me that mri_convert doesn't change the
> orientation of any of the images. It does output the .mat file containing
> the transformation matrix M.
At this point, I can not be 100% certain either as I don't know enough about
the converter. If there is a way of converting your DICOM to NIfTI format
and if you only use NIfTI compliant software throughout, then there should be
no confusion at all.
>
> Then I use SPM5 to slice-time, realign & reslice, normalise, and smooth. I
> have done analyses with defaults.analyse.flip = 0, and = 1. However, the
> results are exactly the same when I compare them. This is not true of some
> patients we scan, whose data we do NOT normalise, but rather co-register w/
> a structural image (e.g. SPGR). The results were flipped based on the value
> of the default.
>
> This got me thinking:
> 1) Does normalising to the template (e.g. T2.nii) automatically flip the
> images? If so, when I run an analysis, will SPM even bother checking
> defaults.analyse.flip?
Not in SPM5. The flipping only happens with obsolete versions of SPM (SPM99
and earlier).
> 2) Does a value of 0 essentially mean "these images
> are in radiological convention; they need to be flipped to be viewed in
> neurological convention"?
"Radiological convention" is a largely meaningless term when it comes to 3D
images that may be stored sagittally. All it refers to is how an axial image
is displayed - which is not necessarily how it is stored.
> 3) Does the value of defaults.analyse.flip affect
> what I see on the screen? e.g. Will I see something different when I use
> the Results, Display, or Check Reg. functions if I change the value?
This defaults.analyse.flip setting only influences how images are treated when
they are not in NIfTI format (or do not have an SPM5 .mat file). If the
image headers does not encode the orientation, then it is a way of telling
SPM what orientation to assume that the data are in.
The "Slices" view from the results confuses many people as it shows an
original slice from the data - rather than a re-oriented slice as seen in the
orthogonal views. If the left and right appear on the wrong sides, then
think of this as the brain being rotated by 180 degrees. The important thing
is to get the mm coordinates correct. Smaller values for the x coordinate
are towardsthe left of the brain.
>
> The reason this is so important, is that it's easy enough when we have a
> patient w/ a lesion to tell which side is which. But on normal subjects,
> even with the Vitamin E pill on their temple, it doesn't show up on the
> functional images. So it's nearly impossible to tell. We also have DTI
> data, that I manually flipped, so that using SPM's Display function, right
> is right and left is left. However, the FA differences and functional
> differences appear to be in opposite hemispheres... and I want to be sure
> if I'm currently doing something wrong/backwards.
If you can get your data into NIfTI format, and use only NIfTI compliant
tools, then there should be no confusion.
Best regards,
-John
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