Dear all,
That's a matter of setting the flip parameter in spm_defaults the right
way. Our raw data is in neurological handedness, so it is 0. No flipping
anymore, everything goes right the first time (handedness is identical
through conversion pipeline PAR/REC>Analyze> Results). Checked with
vitamine marker glued to head.
When you start out with radiological handedness, indeed, you have to
have the handedness flipped during normalization/visualization.
Anyway, it is always a good idea to check your processing pipeline with
something attached to a subjects head the first time you analyze data,
to avoid confusion and double check your settings.
Didn't use Nifti yet, so I definately do another check with a marker on
the head when we one day switch to spm5.
Good luck,
Bas
--------------------------------------------
Dr. S.F.W. Neggers
dept. of Psychonomics,Helmholtz Institute
Utrecht University
Heidelberglaan 2
3584 CS, Utrecht, room 17.09
the Netherlands
Tel: (+31) 30 253 4582 Fax: (+31) 30 2534511
E-mail: [log in to unmask]
Web: http://www.fss.uu.nl/psn/web/people/personal/neggers
--------------------------------------------
Peter Lundberg wrote:
> Dear Spinlanders,
>
> A related peculiarity, using: par/rec -> Analyze format (r2agui) ->
> spm2-analysis -> display_slices.
>
> - When using the procedures above I obtain the anatomical images A/P-
> reversed in the 'glass-brain' of spm2.
>
> - And the background anatomical images in _radiological_ display in
> display_slices, whereas the thresholded activation-(t)-map is in
> _neurological_ display. This is only apparent when there is an
> obvious pathology in the anatomical images. Nevetheless it is
> extremely confusing/misleading/annoying.
>
> Any hope of a resolution in sight?
>
> 73, Peter
>
> On 7 Apr 2006, at 12:53, Bas Neggers wrote:
>
>> Perhaps I may suggest to get rid of DICOM (and associated horrors) in
>> the first place, very well possible when using Philips scanners. After
>> scanning we always convert data to the raw Philips PAR/REC format using
>> the Philips research tools on the console, and then use our
>> converter to
>> convert them to Analyze (with easy to use user interface):
>>
>> r2agui.sourceforge.net
>>
>> I heard that converting Analyze to nifti is easy, but I didnt use
>> nifti yet.
>>
>> DICOM really s*cks for fMRI...
>>
>> cheers,
>>
>> Bas
>>
>> Zhi Wang schreef:
>>
>>> Hello, SPMers:
>>> I want to transform the philips dicom file to Nifti format using the
>>> dicom import in spm5. But I can't. Why? The attached file is the dicom
>>> file!
>>> Also, the images in each volume are interleaved. How can I change the
>>> image order into the correct order. For example, there are 24 slices
>>> in each volume,
>>> the original order:1 2 3 4 5 ......21 22 23 24
>>> the correct order:1 13 2 14 3 15 4...... 12 24
>>> That is to say, I want to change the 13.dcm(original) to 2.dcm and the
>>> 2.dcm(original) to 3.dcm ......
>>> Is there any kind of such software? The MRIcro can't do this.
>>> ---------------------------------------------------------------------
>>> ---
>>> Zhi Wang
>>> 2006-04-07
>>
>
> @ @
> ..
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> | Peter Lundberg Ph: (+46 13) 22 27
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