The mni_icbm152_gm_tal_nlin_asym_09c contains a map of grey matter, rather than a set of labels showing which brain structures to expect.  If you use the "spm_atlas('query','neuromorphometrics',XYZmm(:,i))" as Guillaume suggested, then this makes use of

1. tpm/labels_Neuromorphometrics.nii - An MNI-space NIfTI image encoding brain structures by different numbers. You can see this image using the Display or Check Reg buttons (setting interpolation to NN).
   
2. tpm/labels_Neuromorphometrics.xml - A human readable file that relates the numbers in the NIfTI image to structure names.

Best regards,

-John

---

From: SPM (Statistical Parametric Mapping) <[log in to unmask]> on behalf of sudhakar Mishra <[log in to unmask]>
Sent: 04 September 2019 13:57
To: [log in to unmask] <[log in to unmask]>
Subject: Re: [SPM] Any database or excel sheet describing regions given the coordinates.

 

Dear Guillaume,

The shared solution for the anatomical labeling is working file. However, I am facing problem in adding ICBM152 brain atlas.

I am not sure but is it the xml file required for the labeling as the label which I am getting as answer has no mention of region name in xml file.

I am getting the error: Unknown atlas "mni_icbm152_gm_tal_nlin_asym_09c". However, I have added the nii file in the atlas directory inside spm12 directory.

I am not able to figure out what is missing.

Thanks,

Sudhakar Mishra

Research Scholar

On Wed, Sep 4, 2019 at 5:04 PM Flandin, Guillaume <[log in to unmask]> wrote:

Dear Sudhakar,

Here are some lists of cortical and subcortical atlases:
  https://en.wikibooks.org/wiki/SPM/Atlases

https://www.lead-dbs.org/helpsupport/knowledge-base/atlasesresources/cortical-atlas-parcellations-mni-space/

Have also a look at the JuBrain Anatomy Toolbox:

https://www.fz-juelich.de/inm/inm-7/EN/Resources/_doc/SPM%20Anatomy%20Toolbox_node.html

From within SPM, you can query the Neuromorphometrics atlas given a list
of coordinates:

XYZmm = [
    0.5619   -9.1031   -4.7629
    1.0137  -24.1197    9.3815
   30.0000   -3.0000   -9.0000
  -43.0914  -64.0125   36.7529
    5.1065   39.6984  -23.9468
  -36.5659   30.1030   31.8909
   30.0947  -77.4345  -14.5599
  -47.9653  -31.1684   19.9621
    6.0045    5.7357   53.3664
  -44.0259  -22.1028    8.9601]';

for i=1:size(XYZmm,2)
    spm_atlas('query','neuromorphometrics',XYZmm(:,i))
end

ans =

    '3rd Ventricle'
    'CSF'
    'Right vessel'
    'Left AnG angular gyrus'
    'Right GRe gyrus rectus'
    'Left MFG middle frontal gyrus'
    'Right OFuG occipital fusiform gyrus'
    'Left PO parietal operculum'
    'Right SMC supplementary motor cortex'
    'Left Cerebral White Matter'

Best regards,
Guillaume.


On 04/09/2019 04:58, sudhakar Mishra wrote:
> Hi SPM,
>
> I am looking for any database with python API or excel sheets which has
> description about the regions along with its coordinates. I have a long
> list of coordinates and putting these coordinates one by one in any
> online tool to get the region is not feasible.
>
> If information about the database API or excel sheet is available with
> anyone please share with me.
>
> Thanks
>
> Best,
> Sudhakar Mishra
> Research Scholar
>

--
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
UCL Queen Square Institute of Neurology
London WC1N 3BG