dear spmers.
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.
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.
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)?
how can i be sure after messing around with the default settings that the
epi image orientation is still in line with the dcm images?
i know these are a lot of dummy questions, but i habe to check this out
properly to answer the results of my paradigm. right now, after all these
orientation flips i can not be sure, the side of activation in my epis are
correct.
i hope some one helps and give me (not familiar with all the different
image formats) an idea, how converting dicom data works properly.
thanks a lot
markus burgmer
university of münster, germany
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