Daniel's Home Page

Computer Engineer
Email: glend at mail.nih.gov
Phone: 301-451-6236

Current and past projects:

Atlases, templates and spaces:

Latest AFNI atlas framework changes:

AFNI Atlases


Alignment across two sessions (special case):


Compiled AFNI Matlab applications:


Compiled Matlab programs for RETROICOR correction.


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


and in HBM 2008 PDF here


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.

Example below of DTI fiber tractography volumes rendered with AFNI from data processed with AFNI and DTIStudio.

Downloadable files: