Pulling microarray data by MNI coordinates

Question

How can I write a query in RESTful to get human micro-array data by MNI coordinate?

I would like to pull a CSV of all the microarray measured gene expression levels within a volume of MNI space. Or by structure but with the MNI coordinate each micro array sample came from.

Answer 1

These are provided in the zipped spreadsheets you can download here:

http://human.brain-map.org/static/download

There are mni_x, mni_y, and mni_z columns in the samples spreadsheet.

Via RMA, you can download the T1->MNI affine transform for a given a donor (e.g. name H0351.2001, id 9861) as follows:

http://api.brain-map.org/api/v2/data/Specimen/query.xml?criteria=[name$eq'H0351.2001']&include=alignment3d

The return can be reshaped into a matrix like this (MATLAB syntax):

M = [ x.tvr_00 x.tvr_01 x.tvr_02 x.tvr_09;
      x.tvr_03 x.tvr_04 x.tvr_05 x.tvr_10;
      x.tvr_06 x.tvr_07 x.tvr_08 x.tvr_11 ];

Then you can take a sample's T1 XYZ coordinates, premultiply with that matrix, and you have coarse MNI coordinates.