Non-Growing Tutorial
Step by step procedures for Voxel Based Registration using CMFreg for Slicer 4.3 nightly build
All procedures for voxel based registration have now been incorporated as a modules in the CMFreg extension for Slicer software.
Step 1 – Construct surface models of the cranial base for T1 and T2 images on ITK-snap
CBCT T1 and cranial base segmentation constructed on ITK-snap
CBCT T2 and cranial base segmentation constructed on ITK-snap
Step 2 - Perform cranial base registration for T1 and T2 images using the growing or non growing modules of CMF reg in Slicer depending on whether the patient is growing (child) or non-growing (adult).
Step 2a - Open Slicer software and load the data (CBCTs and Segmentations)
Open Slicer and click on 'DATA' on the upper left.
A new window appears, click in 'Choose File(s) to Add'. Another new window appears allowing you to search for your files. After finding them, select them and click in 'Open'.
A new window appears showing the files that you loaded. Double check if they are the right files and make sure to center them by clicking at the centered checkbox option, this will help to reduce computing time. To finish click in 'OK'.
Step 2b - Select the loaded files into the CMF registration - Growing or NonGrowing module.
After you download the CMFreg extension for Slicer, you can find the CMF Registration module by clicking at the toolbar which is localized at the right side of the loupe. And inside the CMF Registration you can choose Growing or NonGrowing Registration depending of your cases.
The first options to be set are the 'Input Files' where you can see the 'Baseline Scan (fixed)', 'Baseline Segmentation (fixed)', 'Follow up Scan (moving)' and 'Follow up Segmentation (moving)'.
Baseline Scan (fixed) should be your CBCT Time 1
Baseline Segmentation (fixed) should be the single label skull-base segmentation that you created on ITK-snap.
Follow up Scan (moving) should be your CBCT Time 2
Follow up Segmentation (moving) should be the single label skull-base segmentation that you created on ITK-snap.
Step 2c - Select the 'Output Registration Matrix':
The Registration Matrix will be the output text file (.txt), which contains the x,y,z translation and rotation coordinates to register the CBCT and Segmentation files of the 2 time points.
In this tab, click in 'Create new LinearTransform'
Step 2d - Select the 'Apply Registration Matrix':
In this tab, we will select the CBCT and segmentation to apply the registration matrix:
'Input Seg to be Registered' is any segmentation (single or multiple color-labels), which the Registration Matrix will be applied to. It means that it should be a segmentation constructed from the CBCT Time 2.
'Output Registered Seg' is the same segmentation selected as the 'Input Seg to be Registered', that now will be renamed and have the Registration Matrix applied onto. For this option select 'Create new Volume" and rename file with -reg suffix.
'Output Registered Scan' is the CBCT Time 2 that will now have the Registration Matrix applied to. For this option select 'Create new Volume' and rename file with -reg suffix.
Step 2e -After selecting all options in steps 2a to 2e, click in 'Apply' and wait for the status to be Completed. This step will compute the Registration MAtrix and apply it to to the CBCT and segmentation at Time 2.
Double check if the Registration worked properly: compare and scroll through all semitransparent slices of 'CBCT T1'(selected at the 'Baseline Scan (fixed') and 'Output Registered Scan' (selected as 'Output Registered Scan').
This is a example of two CBCT's being compared before and after a Growing Registration using CMF module.
Observation: Slicer do not save files automatically. To have the files saved on the computer click in 'File' on the upper left corner and then in 'Save'. A new window will appear allowing the user to modify the file name, format and directory.
For more information about ITK-snap.
For more information about 3D Slicer
For more information about the CMFreg documentation.
For access the CMFreg source code.