Create dMRI Template




Introduction


    The following steps detail how to create a new human dMRI template from your DWI data.

Step 1. Get the template T1W image


    The template T1W image should be a NIFTI file, and its header should record a transformation matrix to the standard space. An example of this T1W image is the ICBM2009a T1W image (included in the DSI Studio package as mni_icbm152_t1_tal_nlin_asym_09c.nii.gz) .

Step 2. Warp ICBM2009a T1W to T1W image


    You may use any tool to warp ICBM2009a T1W to the template T1W image. 

    DSI Studio also provides a nonlinear normalization tool under [Tools][O7: Nonlinear Registration ToolBox] to complete this task.

Step 3. Apply warping to QA and ISO map


     Apply the warping from Step 2 to HCP1065.ISO.nii.gz and HCP1065.QA.nii.gz (included in the DSI Studio package. In Mac, right-click on dsi_studio_64.app and check package content) so that they will be normalized to the same template space of the T1W from Step 1. Save the normalized images as XXX.ISO.nii.gz and XXX.QA.nii.gz. The XXX can be any name, but the other extension should be the same.

     If you use [Tools][O7: Nonlinear Registration ToolBox] in Step 2, you can apply the warping to QA and ISO images using [File][Apply to warp].

Step 4. Install new template

     Copy the files to the same folder of the HCP1065 files. If there is a cortical segmentation based on the template T1W, copy it to the \atlas folder, and in \template, create a text file named XXX.QA.nii.gz.atlas.txt to record its base file name (You may check out how other templates are associated with their atlases).

Step 5. Construction of a dMRI template.

    Restart DSI Studio and reconstruct your SRC files (see Read DICOM, NIFTI, Bruker 2dseq, or Varian FDF Files to create SRC files). Please follow the steps in Diffusion MRI Reconstruction in DSI Studio and select [Step T2b(1)][QSDR] as the method and select the newly created template at [Step T2b(1)][QSDR][Template]. Make sure to check [Step T2b(2)][ODFs].

     After getting FIB files from all SRC files, the FIB files can be averaged into a population average template using [Tools][O8: Create template/skeleton]. 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. 

Reference

[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: 


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