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SPM  February 2017

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Subject:

Re: How to view MNI coordinates of ROI

From:

Guillaume Flandin <[log in to unmask]>

Reply-To:

Guillaume Flandin <[log in to unmask]>

Date:

Thu, 9 Feb 2017 19:55:10 +0000

Content-Type:

text/plain

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text/plain (196 lines)

Dear Vasudev,

We should think of making this easier in SPM. Maybe CAT12 has already
some dedicated tools but one thing you can try is the following:
* Display results in the usual way ("Results" button)
* Click on SPM Figure > Results Table, to open the satellite window
* Click on the "whole brain" button to have the results table in the
satellite window
* Click on overlay > sections and select an image (eg a structural image
in the same space than your mesh)
* Click on Tools > Rotate 3D, to disable it
* Right click on the MRI image and select
  Display > Labels > Neuromorphometrics
* Now click on the xyz coordinates in the satellite window and see their
label according to the atlas in the Graphics window.

Now that I said all of that you can also just click on
  Atlas > Label using > Neuromorphometrics
and do a right click on the xyz coordinates to see their label...
Note that this will use a volumetric atlas and not a surface based one.

Best regards,
Guillaume.


On 09/02/17 13:50, Dev vasu wrote:
> Dear Jacek,
> 
> I have used CAT 12 toolbox for pre-processing and surface level analysis
> , CAT 12 uses *Desikan-Killiany Atlas and **Destrieux Atlas , *I have
> tried to overlay the surf.gii files in SPM -> canonical folder and i
> could not see any results , but i am able to locate the MNI coordinates
> to anatomical region .
> 
> 1. http://imgur.com/696LzzQ
> 2. http://imgur.com/NKhniap
> 3. http://imgur.com/696LzzQ
> 
> 
> Thanks
> vasudev
>  
> 
> On 9 February 2017 at 14:26, Jacek Matuszewski
> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
> 
>     Dear Vasudev,
> 
>     I thought about overlaying your results from results window when you
>     look at your data. In left bottom results window you have option to
>     project your Statistical Parametric Map from your model on a T1,
>     render or something else. There you should have option to use atlas
>     labels as I described.
> 
>     What you usually do is select contrasts of interest, threshold it
>     and then you have Display subsection of Results window, you select
>     overlays...sections, window pops up - you go to your SPM12 folder -
>     cannonical - single_subj_T1.nii and you should have your results
>     projected on a T1 image.
>     It works for VBM and fMRI clusters, I'm not sure about surface data
>     since I have never analysed those and your preprocessing may not be
>     optimal for standard SPM build-in atlas.
> 
>     Best,
> 
>     Jacek
> 
>     On 2017-02-09 14:13, Dev vasu wrote:
>>     Dear Jacek,
>>
>>     I have done surface based analysis using CAT 12 , thats how i got
>>     previous results, and when i tried to overlay , i could not
>>     visualize anything at all , kindly look into the results in this
>>     picture http://imgur.com/liB69pO .
>>
>>
>>     Thanks
>>     Vasudev
>>
>>     On 9 February 2017 at 13:46, Jacek Matuszewski
>>     <[log in to unmask] <mailto:[log in to unmask]>>
>>     wrote:
>>
>>         There are different atlases informing baout brain structures
>>         in certain MNI coordinates.
>>
>>         If you are using SPM12 you can project results on a section,
>>         i.e. single subject T1 from SPM12/ cannonical folder and right
>>         click on it, select Display - Labels - Neuromorphometrics and
>>         get brain structure from coordinates of you crosshair.
>>
>>         Best,
>>         Jacek Matuszewski
>>
>>
>>
>>         On 2017-02-09 13:26, Dev vasu wrote:
>>>         Dear Jacek,
>>>
>>>         The results are from whole brain analysis , I would like even
>>>         ask you one more question pertaining ROI if there is any way
>>>         i can know which specific ROI that MNI coordinates correspond
>>>         to, Is there online tool that i can use to see the specific
>>>         ROI region  where i see the peak ?.
>>>
>>>         Thanks
>>>         Vasudev
>>>
>>>         On 9 February 2017 at 13:13, Jacek Matuszewski
>>>         <[log in to unmask]
>>>         <mailto:[log in to unmask]>> wrote:
>>>
>>>             Dear Vasudev,
>>>
>>>
>>>             If that is a region of interest that you have build based
>>>             on literature or something else then you should know the
>>>             shape and MNI coordinates for it's center.
>>>
>>>             If these are results of whole-brain analysis MNI
>>>             coortinates of each cluster peak are the last 3 columns
>>>             in spm output table (mm mm mm). You can also right-click
>>>             on the glass brain, select go to nearest local maximum in
>>>             certain cluster and check coordinates at the bottom of
>>>             results window in SPM (coordinates x y, z)
>>>
>>>              But generally you have 2 clusters and 1 voxel and MNI
>>>             coordinates of peaks of those 2 culsters are
>>>
>>>             9 9 50 (for 168 voxels cluster) and 32 16 10 (24 voxels
>>>             cluster)
>>>
>>>             Numbers correspond to X, Y and Z respectively.
>>>
>>>             Best,
>>>
>>>
>>>             Jacek Matuszewski
>>>
>>>
>>>
>>>             On 2017-02-09 12:35, Dev vasu wrote:
>>>
>>>
>>>                 Dear all ,
>>>
>>>                 Is there any way to check the MNI coordinates of ROI
>>>                 where i can see statistical significance as shown in
>>>                 the figure in this link http://imgur.com/a/CIGvv.
>>>
>>>
>>>                 Thanks
>>>                 Vasudev
>>>
>>>
>>>             -- 
>>>             Laboratory of Brain Imaging (LOBI)
>>>             Neurobiology Center
>>>             The Nencki Institute of Experimental Biology
>>>             Pasteur 3, 02-093 Warsaw, Poland
>>>             Tel.: +48 22 5892 551 <tel:%2B48%2022%205892%20551>
>>>             mail: [log in to unmask]
>>>             <mailto:[log in to unmask]>
>>>             website: http://lobi.nencki.gov.pl/
>>>
>>>
>>
>>         -- 
>>         Laboratory of Brain Imaging (LOBI)
>>         Neurobiology Center
>>         The Nencki Institute of Experimental Biology
>>         Pasteur 3, 02-093 Warsaw, Poland
>>         Tel.: +48 22 5892 551
>>         mail: [log in to unmask] <mailto:[log in to unmask]>
>>         website: http://lobi.nencki.gov.pl/
>>
>>
> 
>     -- 
>     Laboratory of Brain Imaging (LOBI)
>     Neurobiology Center
>     The Nencki Institute of Experimental Biology
>     Pasteur 3, 02-093 Warsaw, Poland
>     Tel.: +48 22 5892 551
>     mail: [log in to unmask] <mailto:[log in to unmask]>
>     website: http://lobi.nencki.gov.pl/
> 
> 

-- 
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG

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