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Current and past projects for Daniel Glen

Computer Engineer

Current and past projects:

Atlases, templates and spaces:

Latest AFNI atlas framework changes:

http://afni.nimh.nih.gov/sscc/dglen/AFNIAtlases

http://afni.nimh.nih.gov/sscc/staff/glend/README.atlas.html

Alignment across two sessions (special case):

http://afni.nimh.nih.gov/sscc/dglen/alignmentacross2sessions

Compiled AFNI Matlab applications:

http://afni.nimh.nih.gov/sscc/dglen/CompiledMatlab

Compiled Matlab programs for RETROICOR correction.

http://afni.nimh.nih.gov/sscc/dglen/McRetroTS

Anatomical to EPI registration: align_epi_anat.py script. The program uses the lpc algorithm described here:

http://dx.doi.org/10.1016/j.neuroimage.2008.09.037

and in HBM 2008 PDF here

http://afni.nimh.nih.gov/sscc/rwcox/abstracts/

The data below shows EPI data as it was acquired overlaid on top of the edge-detected anatomical data in colorized edges. On the right is the original data. On the left, the EPI data that has been aligned to match the anatomical data. Here alignment started off fairly close, but was improved by the alignment. Various visualization strategies can be used to assess alignment including the one shown below. In this case, the aligned EPI data follows the anatomical edges much more closely than before alignment. For visualization, the -AddEdge option to the align_epi_anat.py script produces images as produced in the NeuroImage paper link above.

Obliquity: How to deal with oblique datasets in AFNI. Dealing with Obliquity in AFNI

DTI-Query - DTI Tractography program by David Akers and Anthony Sherbondy at Stanford. Integration with AFNI. See http://afni.nimh.nih.gov/sscc/dglen/DTIQuery

Diffusion Tensor Imaging - developed non-linear model that allows for noise in the diffusion weighted images.

PDF presentation, April 19, 2005. Diffusion Tensor Estimation Method

Anisotropic smoothing technique. Rotationally invariant method. The 3danisosmooth program and method are described here

3danisosmooth PDF and in the Presentations folder.