dglen's Home

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Current and past projects for Daniel Glen

Daniel Glen

 

Diffusion Tensor Estimation Method

PDF presentation of our method to estimate the diffusion tensor given April 19, 2005

DTI fiber volume

Rotating DTI fiber volume

DTI fibers spin up and down

DTI fibers

Original DWI B0 data

 

Anisotropic smoothed B0 data

 

Original DWI B0 data

 

Anisotropically Smoothed B0 data

 

Anisotropic smoothing of DWI data

 

Vascular Rendering

Data made with eroded automask and anisotropically smoothed. It was then reversed, thresholded in overlay and placed over original automasked volume.

Funniest NIMH Poem Contest 2006

This poem received second place in the very prestigious Funniest NIMH Poem Contest. For this, Daniel Glen was honored with an "odd" frame / suggestion box. (He was robbed, I tell ya, robbed...)

Vascular Rendering 2

 

Integration of AFNI with DTI-Query

Using DTI-Query with data from AFNI

Compiling DTI-Query

How to build DTI-Query for various platforms

DTI Query on Mac Screenshot

 

DTI Query Binary Files

DTI-Query binary files in tgz format. Extract with tar xzvf dtiqueryaaaa.tgz in the directory for the original files.

DTI-Query tractography available

DTI-Query - the DTI fiber tractography program by David Akers and Anthony Sherbondy at Stanford is available for AFNI users

Dealing with Obliquity in AFNI

Dealing with obliquely acquired data - commands and concepts

Oblique to Cardinal transformed EPI

 

Cardinal to Oblique transformed anatomical data

 

Obliquity in AFNI

How to deal with oblique datasets in AFNI

Unaligned EPI data over anat edges

Underlay edge detect and color. Overlay monochrome green color scale with auto-range off.

Aligned EPI data over anat edges

Underlay anat - edge detect and color. Overlay in monochrome green colorscale.

Aligned EPI data over anat edges

 

Unaligned EPI data over anat edges - Green

 

Aligned EPI data over anat - pre and post alignment

To create this image, the underlay is set to edge detect in display menu, Color, Swap. Right-click color bar and set Zero color to black. For overlay, right-click overlay color bar, and select a monochrome scale like this gray_circle or one like red_monochrome or green_monochrome. With sub-bricks for overlay and threshold set to the same epi dataset sub-brick, set lower threshold or "auto threshold" on overlay. Turn off auto-range and set range to useful maximum.

Compiled Matlab Applications in AFNI

Several Matlab applications are available as stand-alone applications

McRetroTS - Matlab compiled version of retroTS.m

Use McRetroTS for cardio-respiratory regression with fMRI data as standalone application without Matlab

Atlases in AFNI - framework

How AFNI handles atlases, templates, spaces and transformations

Alignment of EPI data across two sessions

The special case of aligning EPI data across two sessions without bias toward either session