Thanks for elaboration. It was helpful. Since both the coordinates and anatomical labeling template are in MNI system, the neuromorphometrics labeling will work. Best, Sudhakar Mishra Research Scholar IIIT-Allahabad Website <https://brainnetworkresear.wixsite.com/brainnetworks> On Wed, Sep 4, 2019 at 8:30 PM Ashburner, John <[log in to unmask]> wrote: > 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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikibooks.org%2Fwiki%2FSPM%2FAtlases&data=02%7C01%7C%7C2cb54c47bc844dd04dc708d731376e02%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637031986445855856&sdata=rRzuyDgV4od7NGSKhFuBmclU%2Fs9gpY9Idh0MJvemknQ%3D&reserved=0> > > > https://www.lead-dbs.org/helpsupport/knowledge-base/atlasesresources/cortical-atlas-parcellations-mni-space/ > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.lead-dbs.org%2Fhelpsupport%2Fknowledge-base%2Fatlasesresources%2Fcortical-atlas-parcellations-mni-space%2F&data=02%7C01%7C%7C2cb54c47bc844dd04dc708d731376e02%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637031986445860857&sdata=%2BNU7m6Fr0LTmcRXJ8vQpnkQmE8a%2FS2K1JvjYkQghvxM%3D&reserved=0> > > 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 > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fz-juelich.de%2Finm%2Finm-7%2FEN%2FResources%2F_doc%2FSPM%2520Anatomy%2520Toolbox_node.html&data=02%7C01%7C%7C2cb54c47bc844dd04dc708d731376e02%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637031986445865851&sdata=I8kmeRYja3P8fYctXkzI52S5IOR3T2WRix4dkRcmpsw%3D&reserved=0> > > 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 > >