...

All T1 images were registered to MNI space. FreeSurfer's affine registration was used for the in cranio scans. For ex cranio brains, the T1 was first rigidly aligned using FSL (Jenkinson, et. al, 2002) and then non-rigidly aligned using ANTS (Avants, et. al., 2011). The 3-D affine transform from a location in the MR volume to MNI space is encapsulated in the Alignment3d model.

Examples queries:

• Download links for MR and DTI data Download the MR to MNI transform parameters

  Code Block
  http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor, rma::criteria,products[abbreviation$in'HumanMA','HumanSZ','HumanCtx','HumanSubctx'],organism[name$il'Homo Sapiens'], rma::include,specimens(well_known_files(well_known_file_type[name$in'T1-MRI','T2-MRI','DTI-MRI'])), rma::options[only$eq'donors.name,products.name,well_known_files.download_link,specimens.id']

• Download TI MR scan for donor 'H0351.2002'

  Code Block
  http://human.brain-map.org/api/v2/well_known_file_download/157723301

• Download the MR to MNI transform parameters

  Code Block
  http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor, rma::criteria,products[abbreviation$eq'HumanMA'], rma::include,specimens[parent_id$eqnull](alignment3d),rma::options[only$eq'donors.id,donors.name,specimens.id']

Figure: T1 MR scan for donor 'H0351.2002'

...