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
* 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.
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
> 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.
> 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 .
>> On 9 February 2017 at 13:46, Jacek Matuszewski
>> <[log in to unmask] <mailto:[log in to unmask]>>
>> 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.
>> 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 ?.
>>> 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
>>> Numbers correspond to X, Y and Z respectively.
>>> 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.
>>> 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