Markus Burgmer wrote:
> sorry that i havo to ask about image orientation again. i tried the
> archives, but all the messages i read got me more confused than before. my
> problem is as follows:
> i convert my dicom data (t1 and epi) with mricro, without any right to left
> flip. the conversion of the t1 image is a little bit confusing, due to the
> sagittal slices. but i managed this with the "save as" and "sagittal-left"
> options. afterwards the orientation seems top be ok, with right to right
> (=neurological orientation).
> in mricro the epi image is in radiological orientation
> (mricro gives two message before showing the image:
> note: this nifti file specifies an affine rotation [qform > 70]. mricro
> will display raw data.
> warning: this nifti image includes an rotation transformation. you should
> reslice this data before attempting to overlay the image)
>
> i checked the orientation of the t1 and the epi images in spm5 without any
> step of preprocessing and both images are not in line, the same as in
> mricro, but the other way round now.
Hi Markus,
Can I first say that if you're using SPM5, it will be much better to
convert to NIfTI, e.g. using the SPM5 DICOM to NIfTI conversion rather
than converting to Analyze with mricro. Alternatively, check out Chris
Rorden's (author or MRIcro) dcm2nii
http://www.sph.sc.edu/comd/rorden/mricron/dcm2nii.html
> john ashburner gave me advice about a nearby problem (with the aal tool),
> but unfortunately i deleted the email. he mentioned something about the
> default settings change from 1 to 0. after this, only the orientation of
> the t1 image is flipped and is in line with the epi image now.
This is the defaults.analyze.flip flag near the start of
spm_defaults.m, although which setting you want for it can be a rather
complicated issue... It's safest if you can find an image where you
know which side is left/right, e.g. from scanning with an oil-capsule
attached to the head, then the right side of the brain should have
positive x-coordinate when you display the image in SPM5.
> but what exactly means the change in the settings?
> i read in an answer about orientation problems in spm99, that after
> normalization the orientation will changed again.
> is there a document which describes the orientation problem and its special
> settings between different programs (mricro, spm) and within one program
> (spm)?
This page is very helpful:
http://www.grahamwideman.com/gw/brain/orientation/orientterms.htm
Best of luck,
Ged.
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