Dear Mark
Thanks a lot for your advice.
I have realized that all templates of FSL, SPM, and also those of FreeSurfer
(.mgh files) have negative q-factors in their NIFTI (or MGH) headers and, as
a consequence, also negative determinates of the q-form matrices.
Therefore I was worry about that images were differently oriented depending
on the tool used for file conversion (.par/.rec to nifti). I used a marker
during scanning and the labels in fslview are correct for both images,
although the q-factors of their headers are different.
When using fslreorient2std, the images can be transformed into fsl standard
orientation. Without this transform, images are displayed e.g. upside down
(relative to fsl templates) in fslview, although the labels (A, P, R, L, I,
and S) are always correct, regardless whether the images are shown in a
"convenient" (standard FSL) way.
In some of my projects I used combined software tools such as FSL and
FreeSurfer or FSL and TrackVis or FSL and SPM / inhouse MATLAB scripts and I
hope to minimize orientation problems when forcing my raw data orientations
to negative q-factors as seem to be "standard" in these tools (templates are
oriented in this way).
As I understand you right when using e.g. fslmaths or fslstats or other
fslfunctions with radiological and neurological oriented (as determined by
fslorient -getorient) images simultaneously, which both have correct labels
in fslview, there should be no problem.
Cheers
Jürgen
On [DATE], "Mark Jenkinson" <[ADDRESS]> wrote:
> Dear Jurgen,
>
> The q-factor can be positive or negative and still be correct. It is only the
> labels that matter. So look at the labels in FSLView and see if they are
> correct. If they are fine then you don't need to worry about the details of
> the nifti qform or sform (as long as at least one has a non-zero code,
> otherwise it means that there is no information stored, which is dangerous).
>
> If you see something that appears flipped with respect to the labels in
> FSLView, then that is a problem and you'll need to do something about it in
> conversion or by modifying the nifti information if you can determine how they
> should be fixed.
>
> All the best,
> Mark
>
>
> On 11 Jan 2013, at 13:07, Jürgen Hänggi <[log in to unmask]> wrote:
>
>> Dear FSL experts
>>
>> Please can you confirm that the NIFTI q-factor in the NIFTI header has to be
>> negative (e.g. -1) in order to have correct right and left orientation.
>>
>> When the NIFTI q-factor is positive in my T1-w. and DTI images, then the
>> left and the right hemisphere seem to be flipped.
>>
>> Thanks in advance
>> Regards
>> Jürgen Hänggi
>>
>> ----------------------------------------------------------------------------
>> Jürgen Hänggi, Ph.D.
>> Division Neuropsychology
>> Institute of Psychology
>> University of Zurich
>> Binzmuehlestrasse 14, PO Box 25
>> 8050 Zurich, Switzerland
>> 0041 44 635 73 97 (phone office)
>> 0041 76 445 86 84 (phone mobile)
>> 0041 44 635 74 09 (fax office)
>> BIN 4.D.04 (office room number)
>> j.haenggi[at]psychologie.uzh.ch (email)
>> http://www.psychologie.uzh.ch/neuropsy/ (website)
>> http://www.juergenhaenggi.ch (private website)
>>
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Jürgen Hänggi, Ph.D.
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi[at]psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)
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information. If you are not the intended recipient (or have received this
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