VDW related

3.2.3 Fine-Tuning alignment does not work properly

By default, Fine-Tuning alignment uses the first volume in the data set. It might be, that this is a diffusion weigthed image instead of a b0. The fine alignment fails at this point. The solution is to set the display volume to a b0 volume (see DMR Properties > DWI Data > Volume (b0) for display), and save the DMR. Then, in the alignment procedure, use the AMR as input.

3.2.4 Optional: Manual Co-registration of DMR with VMR

In some cases the position information may be lost or incorrectly read by BrainVoyager. The automatic co-registration will not work, and you are forced to use manual co-registration. In this section, the procedure is discussed step-by-step.

1. Open the VMR corresponding to the DTI data set, human.vmr.
2. Go to DTI-->Coregister DMR-DWI to VMR. Via the Browse button, locate the DMR human31dir.dmr.

   

3. Go to the Source Options tab. In most cases, BrainVoyager has created an AMR file from the first volume, but if this did not happen, choose the use DMR data (DWI Slices), and check the invert intensities box. This has to be checked, since a DWI images has T₂ contrast, while T₁ contrast is needed for co-registration. Check the create edge display for DMR/AMR data box. Next, hit the Create Volume button. This will create a VMR from the first DMR volume.

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4. The window will look like this:

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   On the top row, we see the VMR, overlayed with the slice orientation of the DMR data set (light yellow lines) The bottom rows shows the VMR overlayed with the DMR data. The green lines represent the edges of the DMR data. As is immediately clear, the DMR is scanned in a transversal way, while the VMR is sagittally oriented. We will solve it in the next step, by converting the DMR to sagittal orientation.

5. Click the To SAG button in the co-registration dialog. A dialog pops up:

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   By manipulating the data via the middle buttons, change the right view to a sagittal view. In this case, it means hitting the X: +90 button once, and Y: -90 button one, but in your data it may be different. Check the Framing cube dimension: 256 radio button, and click OK.

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6. Go to the Initial Alignment tab of the coregistration dialog and check the Manual Alignment -- use "To SAG" option. Click Run IA.

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   The result is the DMR in sagittal orientation overlayed on the VMR:

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7. The result is a very crude alignment, so it needs to be adjusted. This is done by transformations and rotations. Go to the coregistration tab of the 3D Volume Tools:

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   Using x, y, z translations and x, y, z rotations, try to align the DMR as good as possible to the VMR data set. In the bottom row of the data display, you can freely browse the data, and this is of course highly recommended. When aligning, concentrate on aligning gyri and sulci rather than the ventricles, since the tissue around ventricles suffers from (large) distortions in EPI data such as DMR. Try to be as precise as possible! For the current data set, the following parameters were found:

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   and the window looks like this:

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8. Now, return to the DMR-VMR coregistration dialog, via DTI-->Coregister DMR/DWI to VMR. Go to the Fine Tuning Alignment tab, and check the Manual alignment -- use current translation and rotation values option:

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   Hit the Run FA button.

9. Result of the manual alignment procedure:

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   BrainVoyager has saved the transformation values in the files human31dir-TO-human_IA.trf and human31dir-TO-human_FA.trf