1.1 --- a/grant.txt Mon Apr 13 19:38:30 2009 -0700 1.2 +++ b/grant.txt Mon Apr 13 20:27:32 2009 -0700 1.3 @@ -9,7 +9,7 @@ 1.4 1.5 (2) develop an algorithm to suggest new ways of carving up a structure into anatomical subregions, based on spatial patterns in gene expression\\ 1.6 1.7 -(3) create a 2-D "flat map" dataset of the mouse cerebral cortex that contains a flattened version of the Allen Mouse Brain Atlas ISH data, as well as the boundaries of cortical anatomical areas. Use this dataset to validate the methods developed in (1) and (2).\\ 1.8 +(3) create a 2-D "flat map" dataset of the mouse cerebral cortex that contains a flattened version of the Allen Mouse Brain Atlas ISH data, as well as the boundaries of cortical anatomical areas. This will involve extending the functionality of Caret, an existing open-source scientific imaging program. Use this dataset to validate the methods developed in (1) and (2).\\ 1.9 1.10 In addition to validating the usefulness of the algorithms, the application of these methods to cerebral cortex will produce immediate benefits, because there are currently no known genetic markers for many cortical areas. The results of the project will support the development of new ways to selectively target cortical areas, and it will support the development of a method for identifying the cortical areal boundaries present in small tissue samples. 1.11 1.12 @@ -175,10 +175,26 @@ 1.13 == Preliminary work == 1.14 1.15 === Format conversion between SEV, MATLAB, NIFTI === 1.16 -todo 1.17 +We have created software to (politely) download all of the SEV files from the Allen Institute website. We have also created software to convert between the SEV, MATLAB, and NIFTI file formats, as well as some of Caret's formats. 1.18 + 1.19 1.20 === Flatmap of cortex === 1.21 -todo 1.22 +We created a mask which selects only those voxels within the ABA atlas space which belong to cerebral cortex. 1.23 + 1.24 +todo 1.25 + 1.26 +Using Caret, \cite{van_essen_integrated_2001} 1.27 + 1.28 +We manually entered the boundaries of each cortical area into Caret. 1.29 + 1.30 +Cortical layers are found at different depths in different parts of the cortex. We have manually demarcated the depth of the outer boundary of cortical layer 5 throughout the cortex. 1.31 + 1.32 +In preparation for extracting the layer-specific datasets, we have extended Caret with routines that allow the depth of the ROI for volume-to-surface projection to vary. 1.33 + 1.34 + 1.35 + 1.36 + 1.37 + 1.38 1.39 1.40 1.41 @@ -228,6 +244,9 @@ 1.42 1.43 todo 1.44 1.45 +\vspace{0.3cm}**Areas can sometimes be marked by underexpression** 1.46 + 1.47 +todo 1.48 1.49 === Specific to Aim 1 (and Aim 3) === 1.50 \vspace{0.3cm}**Forward stepwise logistic regression**