[caret-users] Q) Why is the metric of right hemisphere showing up in the left hemisphere only?

Fri Apr 10 10:22:43 CDT 2009

Hi YSL,

If I understand you correctly, then, Caret is mapping the data 
correctly; however, when you try to view both hemispheres concurrently 
in Caret, the metric map does not match with the proper hemisphere as 
effortlessly as you would like.

I have only one suggestion:  Try viewing just one of the hemispheres by 
itself, to remove any cross-hem confounds in the visualization.  If you 
still see a mis-match, then the mapping itself is flipped.  If you don't 
see a mis-match, then you can rule out the mapping.

Beyond this, I can't personally help, because I don't view both hems 
concurrently.  I know only what is in the tutorial (and have forgotten 
that).

Donna

On 04/10/2009 09:42 AM, Yune S. Lee wrote:
> 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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