Dear Peter, List,
well, as far as I understand it, flipping formally refers to a
handedness change of your coordinate system from a left-handed to a
right handed one. Which, indeed, in spm2 comes down to LR flipping, but
only when you have your images in axial orientation with the cerebellum
at the bottom of your slice, when looking at it. Your AP flipping is
probably a rotation, not a handedness change... some converters
interpret the data differently with regard to image orientation, but not
handedness, as far as I have seen, so it doesn't matter that much when
you manually realign your data before preprocessing (which is a good
idea anyway). This rotation could be reversed with a simple rigid body
rotation of pi radials using spm. But maybe I am wrong, just my 2 cts.
At least, that is what we see after converting Philips data, might be
different for your pulse sequence, I am not an MR physicist.
In our PRESTO scans normal vitamine capsules were visible quite well (I
do not know more details, they always ly around in the scanner control
room here).
Good luck,
Bas
Peter Lundberg wrote:
> 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
|