Hi again,
1. The defaults.analyze.flip spm2-parameter seems to refer to R/L
flips (not A/P flips which was one of the observations)?
2. We have never been able to find a suitable geometry (positive)
marker that is visible in our GRE-EPI under the conditions of an fMRI
experiment. Neither of vitamine-E, mustard, CuSO4(aq), etc worked.
Any suggestions?
3. What does a default setting of defaults.stats.maxres = 64 imply
(image matrix size?)?
73, Peter
On 7 Apr 2006, at 15:07, Bas Neggers wrote:
> 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
>>>
>>
>> @ @
>> ..
>> ==================================================ooOO==========OOoo=
>> === =====
>> | Peter Lundberg Ph: (+46 13) 22 27
>> 90 |
>> | MR-Unit Fax: (+46 13) 22 27 92 (alt 22 47
>> 49) |
>> | Dept of Radiation Physics Email:
>> Peter.Lundberg_AT_imv.liu.se |
>> | University of
>> Linkoping |
>> | S-581 85 Linkoping Efax:
>> PeterLundberg_AT_f013222792.fax.sunet.se |
>> | Sweden www: http://www.imv.liu.se/
>> radiofysik/ |
>> =====================================================================
>> === =====
>> () "To a poet nothing is useless." (SJ) ooOO OOoo
@ @
..
==================================================ooOO==========OOoo====
=====
| Peter Lundberg Ph: (+46 13) 22 27
90 |
| MR-Unit Fax: (+46 13) 22 27 92 (alt 22 47
49) |
| Dept of Radiation Physics Email:
Peter.Lundberg_AT_imv.liu.se |
| University of
Linkoping |
| S-581 85 Linkoping Efax:
PeterLundberg_AT_f013222792.fax.sunet.se |
| Sweden www: http://www.imv.liu.se/
radiofysik/ |
=======================================================================
=====
() "To a poet nothing is useless." (SJ) ooOO OOoo
|