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[edit] Processing Venograms

[edit] Background

The venograms we currently use are 3D-phase contrast [3DPC] gradient echo scans. (See Hornak's online MRI book.) These are contrast scans, which means two images are acquired for each slice. A subtraction of the first half of the images minus the second half of the images gives a volume that accentuates the vasculature.

[edit] Setting up

[edit] Sorting DICOMs

Before executing any code, the two sets of dicoms captured during the venogram scan must be organized into two separate folders:

First half:
Second half:

[edit] Alignment

View the code within alignVenogram. Do not run it as a function; instead, we will be executing portions of the code and taking it a step at a time.

[edit] Setting paths

Execute cell 1 of the code.

All venogram related scans.
e.g., /subject/Venogram/
Dicom files from the t1-SPGR anatomy (ref anatomy)
e.g., /subject/Venogram/t1-SPGR/
First half of the dicom files from the venogram (vessel contrast)
e.g., /subject/Venogram/Venogram/
Second half of the dicom files from the venogram (aligned crude anatomy)
e.g., /subject/Venogram/VenogramAnat/
Path to the stored hi-resolution t1 anatomy (NIFTI file)
e.g., /subject/t1.nii.gz

[edit] Converting DICOMs to NIFTIs

Execute cell 2 of the code.

[edit] Reslicing NIFTIs to resolution of stored t1-anatomy

Execute cell 3, part (a) of the code.

Use this to verify whether the t1 resolution is as expected (e.g., [.8 .8 .8])

Execute cell 3, part (b) of the code.

[edit] Performing alignment

Execute cell 4, part (b.i) of the code.

Perform manual alignment until the two images are suitably aligned. To ease this process, open the Interpolated 3-View Window under “Window” in the toolbar. Alternatively, press ctrl + 7. Check the “Compare Interp / Ref” box, which will allow you to see the two images overlaid for easy comparison.
Once you are comfortable with the manual alignment, you’ll find the most success using the Nestares alignment code. This is located under “Alignment” -> “Fine” -> “Nestares code.” Once it completes the iterations, proceed.

Execute cell 4, part (b.ii) of the code.

Save your alignment settings, store the transformed volume, and close mrRx.

[edit] Applying alignment settings to venogram files

Execute cell 5 of the code.

[edit] Segmentation

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