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Construction of a high angular resolution atlas


DSI Studio provides a way to reconstruct diffusion properties in a standard space using q-space diffeomorphic reconstruction (QSDR). The data in the standard space can be averaged to create a group-average diffusion template for tracking and analyzing representative fiber pathways. 

The following are steps to create a diffusion template using DSI Studio.

1. Convert diffusion data to src files

You may use either the DICOM or NIFTI files to create SRC files. An SRC file stores diffusion images and the gradient table. You can also use command line functions of DSI Studio to batch converting all subject data to src files.

2. Q-space diffeomorphic reconstruction (QSDR)

Click on "STEP2: Reconstruction" and select ALL .src files. In the reconstruction windows, jump to "select reconstruction method". QSDR uses the mask from the build-in template, and you can ignore the mask assignment. 

Select QSDR as the reconstruction method. Here are some parameters that may affect the results.

Diffusion sampling length ratio

This ratio defines the sensitivity of the reconstruction method to fast diffusion. You may need to test between 0.4 to 1.6 and see which parameters work the best for your data. A higher value gives better crossing fiber resolving, but it also increases the sensitivity to noise. A value around 1.2 gives good results, but the optimal value depends on the data. For in-vivo scan on human brain, the value is usually around 1.2. For ex-vivo scan, the value will be lower, ranging from 0.4 to 0.9.

Registration method

CDM is recommended. For human subjects with T1W, you may use T1W-CDM (need to assign the T1W).

You must check "ODFs" in the output box. This will output full ODF data in the fib file that allows further averaging.

3. Averaging ODFs

1) Back to the Main Window, in the Tools: Others tab, click "Step 1: create template/skeleton". 

2) Add in all FIB files and specify the output file name. This dialog outputs two fib files, one without and one with the averaged ODFs. The one without the ODFs can be used as the local tract skeleton for creating a connectometry database.

[1] Yeh, F.C., Tseng, W.Y., 2011. NTU-90: A high angular resolution brain atlas constructed by q-space diffeomorphic reconstruction. Neuroimage 58, 91-99. (pdf)
[2] Yeh, F.C., Wedeen, V.J., Tseng, W.Y., 2011. Estimation of fiber orientation and spin density distribution by diffusion deconvolution. Neuroimage 55, 1054-1062. (pdf)
[3] Yeh, F.C., Tseng, W.Y.Sparse Solution of Fiber Orientation Distribution Function by Diffusion Decomposition”, PLoS One. 2013 Oct 11;8(10):e75747. doi: 10.1371/journal.pone.0075747. (pdf).