[caret-users] Q) Why is the metric of right hemisphere showing up in the left hemisphere only?
Yune S. Lee
yune-sang.lee at dartmouth.edu
Fri Apr 10 09:42:22 CDT 2009
Hi Donna,
Thanks for the comments.
In fact, I use NIFTI format by converting it from PAR/REC, so it is not
affected by default.analyze.flip.
It has the orientation info in it. I use it throughout the preprocessing
and further analysis (2nd level) and so on.
However, what SPM generates after the 2nd level analysis is the analyze
format T image (e.g., SPMT_0001.hdr / img), not NIFTI and this was
what I meant to say "I used analyze format for mapping into caret's
template". But the orientation in the T image is the same as original
NIFTI image.
(I wish SPM generates NIFTI output, not analyze format..)
So, I'm quite sure about the orientation in the SPM rendering view (Left
is left/ Right is right)
In the meanwhile, I found out that I have to change the model every time
I would like to see different hemisphere even after switching from one
view to another in the metric selection. For instance, if I choose
inanimate_conservative_R in the metric selection, I also have to match
the hemisphere in the model
(e.g, inflated human.pas.B12.Right...coord). Then, as I wished, I can
view the activation pattern of the right hemisphere on the right template.
Is it supposed to be the way of how to view? Enclosed is the screen
captured file (so, without changing the model, the 2nd view
(inanimate_conservative_R.hdr) will be shown on the left side.
Again, thanks for your help!
-YSL
Donna Dierker wrote:
> YSL,
>
> The best help I can give is to convince you to switch to NIfTI sooner,
> rather than later. The number of problems like this will decrease
> substantially once you do so. And this is just one example of the types
> of problems NIfTI was intended to solve.
>
> Meanwhile, let me cite the SPM2 compatibility section:
>
>
>> Although SPM2 still uses the Analyze file format, and will therefore
>> read image files from previous versions of SPM, there are differences
>> in the algorithms, templates and models used in SPM2 over previous
>> releases. Therefore, we recommend you use a single SPM version for any
>> given project.
>>
>> One thing to watch out for is the image orientation. The proper
>> Analyze format uses a left-handed co-ordinate system, whereas
>> Talairach uses a right-handed one. In SPM99, images were flipped at
>> the spatial normalisation stage (from one co-ordinate system to the
>> other). In SPM2, a different approach is used, so that either a left-
>> or right-handed co-ordinate system is used throughout. The SPM2
>> program is told about the handedness that the images are stored with
>> by the |spm_flip_analyze_images.m| function and the
>> |defaults.analyze.flip| parameter that is specified in the
>> |spm_defaults.m| file. These files are intended to be customised for
>> each site. If you previously used SPM99 and your images were flipped
>> during spatial normalisation, then set |defaults.analyze.flip=1|. If
>> no flipping took place, then set |defaults.analyze.flip=0|.
>>
>> Check that when using the Display facility (possibly after specifying
>> some rigid-body rotations) that:
>>
>> * The top-left image is coronal with the top (superior) of the
>> head displayed at the top and the left shown on the left. This
>> is as if the subject is viewed from behind.
>> * The bottom-left image is axial with the front (anterior) of the
>> head at the top and the left shown on the left. This is as if
>> the subject is viewed from above.
>> * The top-right image is sagittal with the front (anterior) of the
>> head at the left and the top of the head shown at the top. This
>> is as if the subject is viewed from the left.
>>
>>
> So, in your SPM distribution directory (a subdirectory of your matlab
> distributioin), find the file named like |spm_flip_analyze_images.m and
> look at the ||defaults.analyze.flip setting. If it is set to 1, then
> SPM is writing the images out with right on left, which means you will
> experience the type of flip problem you are seeing with Caret. You can
> get around this problem by using File: Open Data File to open the fMRI
> volume in Caret, and then map to loaded volumes when mapping. When you
> use the Open Data File Dialog, there is a checkbox for flipping SPM
> analyze images with right on left. Check (or de-check) this checkbox,
> and you might be happier with your results.
>
> Don't like having to open the volumes manually this way? Then give
> serious consideration to converting your Analyze volumes to NIfTI -- if
> only for mapping purposes.
>
> The one solution I do *NOT* recommend is to mess with that
> ||defaults.analyze.flip variable, especially if you have created much
> data using this SPM2 release. You will end up with some right-handed
> output, some left-handed, and no good way of knowing which is which. It
> was intended to be set once, and not messed with. Not long after, the
> NIfTI standard came along -- a much better way of specifying flips.
>
> Donna
> |
> On 04/10/2009 08:10 AM, Yune S. Lee wrote:
>
>> Hi Donna
>> Thanks for the answer.
>> Yes, I mapped using analyze header file.
>> While I may use nifti format later on, my question is still that the
>> activation on the right side is represented on the left hemisphere
>> (which I assume
>> it is the way caret is. ) I attach two screen capture file. As shown
>> in the right_hemisphere file, the hemisphere is not changed even after
>> I choose
>> inanimate_conservative_R in the metric selection. However, it looks
>> like the activation pattern looks similar to that shown in the SPM.
>> So, if it's the way caret is, I'm just aware of the fact, or if there
>> is any way to flip the template hemisphere, I would like to know about
>> it as well.
>> Any help would be appreciated.
>>
>> Thanks,
>> YSL
>>
>>
>>
>>
>> Donna Dierker wrote:
>>
>>> Hi YSL,
>>>
>>> I wonder if you are mapping an Analyze header, and you did/didn't
>>> specify a LR flip when opening the volume file?
>>>
>>> If you can convert your volume to NIfTI first, you're better off.
>>>
>>> Donna
>>>
>>> On 04/09/2009 01:20 PM, Yune S. Lee wrote:
>>>
>>>
>>>> Dear Caret users,
>>>> I'm wondering why the activation pattern of right hemisphere always
>>>> shows up in the left hemisphere even after I change from Left to Right
>>>> in the metric selection view. I do see the activation map changes
>>>> depending on which side I choose, so I assume the activation on the
>>>> right side is just showing up
>>>> in the left hemisphere. Yet, is there any way to view the pattern on
>>>> the right hemisphere template?
>>>>
>>>> Thanks in advance,
>>>> YSL
>>>>
>>>>
>>>>
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>>>>
>>>>
>>>>
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