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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