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sample_anatomy_toolbox_demo.m

Copyright 2013 Allen Institute for Brain Science Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

 

      		
    

    

      
        

          
        

        
The SPM Anatomy
Toolbox
has probabilistic maps of Brodmann areas.  This code extracts the sample
expression values for a single probe and then exports the sample
locations in a format that can be read into the toolbox.  This is a PDYN
probe, which you can see by inspecting the probe variable below.

      		
      
        
specimen_name = 'H0351.2001';
probe_name = 'A_23_P40262';

      		
    

    

      
        

          
        

        
Download the specimen and probe expression values.

      		
      
        
probe = download_probe(probe_name);
specimen = download_specimen(specimen_name); 
[samples, explevels] = download_expression(probe.id, specimen.donor_id);

      		
    

    

      
        

          
        

        
Use the batch cytoarchitectonic probabilities
tool to read in the human_ma_samples_MNI.txt file generated below.
Note: the transform from microarray sample locations to MNI space was
computed using simple affine registration.  As a result, anatomical
labels of fine structures produced by the Anatomy Toolbox may not be
completely accurate.  More advanced registration of human brain specimen
to MNI coordinates is recommended for accurate analysis.  


      		
      
        
disp('Exporting sample coordinates to human_ma_samples_MNI.txt');
coords = transform_samples(samples,specimen.alignment3d)';
save human_ma_samples_MNI.txt coords -ascii