Example Registering using Head in Hat Method

Warning

The registration process assumes that the 2 sequences being registered have the same slice thickness.  If they do not, click here for instructions on how to  modify the slice thickness of a data set to match another data set.

Load a central location, for all scanning sequences, from a patient study and use the left button in the Browser Window (see Selecting Images to Display) to check alignment between the scanning sequences. Make a note of which scanning sequences are misaligned and use the following instructions to align.

Note

Delete the browser before continuing with Registration.

Use Split Display in the Display Windows to speed processing during registration.

During registration, ensure that both sequences being registered contain as much of the patient as possible, including the top of the skull without brain.

1. Load all locations of one scanning sequence from a patient study. This will be referenced as the base set into Browser #1.

2. Load all locations of another scanning sequence from the same patient study into Browser #2.  This sequence will be registered to the images loaded into Browser #1.

3. Link the browsers for the two sets.

   Note

   If the contrast between the two sets of images are substantially different, do not link the browsers. You will need to repeat steps 4 - 6 for the second browser with different Hi values.

4. Select Contour in the Region of Interest/Volume of Interest Dialog.

   1. Enter 0 for the Lo value.  To select the Hi value: move cursor over the skin area of the image, observe the initial peak in gray level as the skin area is entered (lower-left of the Display Window).  Choose a Hi value slightly less than this peak (~75% of the value).

   2. Use the left button to select an area outside the skin, the upper-right quadrant of the image works best.  This will display the image contour.  Ensure the contour is smooth and free from gross discontinuities, small breaks in the contour and outlines of the nose and ears will not effect the outcome.  Adjust the Hi value as necessary or erase parts of the contour using Erase Irregular and redraw manually using Irregular.

   Note

   Choosing a different point on the image may drastically change the contour outline.

   Ensure, the Region of Interest Dialog displays the Browser # of the images you are working on.  If necessary, move mouse over desired browser and continue working.  This will reset the Browser # of the Region of Interest Dialog.

5. Press Start Macro, select a point outside the skin, press End Macro, and press Run Macro.
   

6. Use the left button in the Browser Window to check all locations for gross errors between the two sets.

   1. If any gross errors exist, press another point in the incorrect image to repair. If this does not repair the contour enter a different value for the Hi value and press another point in the incorrect image. (Step 4)

   Note

   If you did not link the browsers in Step 3, Repeat steps 4-6 for the second browser with different Hi values.

7. Use the right button in the Browser Window to delete any images that do not have sufficient anatomy.

8. Select Analyze->Registration->Register from the Main Window.

   1. Press Match. The residual value will be displayed in the information window.  Press Match several more times until the residual value reaches a minimum value and then begins to increase..

      Note

      The residual value can vary significantly between patients and even between different sets of the same patient. Do not wait for the residual value to fall below  specific level.

   2. Upon the first increase in the residual value, press Backup.

   3. Press Reslice.

9. Enable the two browsers for Link Displays in the Main Window.

10. Use the left button in the Browser Window to check registration between the two sets, checking ventricles and skull.

    1. Set and Send Link as a in the Main Window to Region.  This will copy the region of interest created in steps b and c to be displayed on both sets of images.

    2. Use Threshold or Slice to draw regions.

    3. Use Edgi to get outline.

If misregistered, delete the browser with the resliced images  and repeat beginning at Step 4. You may need to select different anatomy, other than skin, for the contour or the point used to start the contour may need to be changed.

If registration is successful, delete the browsers for the scanning sequence that was resliced. Start at Step 2 if there are more scanning sequences to register.

Example Registering using the AIR Method

Warning

The registration process assumes that the 2 sequences being registered have the same slice thickness.  If they do not, click here for instructions on how to  modify the slice thickness of a data set to match another data set.

Note

This method uses programs provided by Automated Image Registration package (alignlinear) from UCLA.

Load a central location, for all scanning sequences, from a patient study and use the left button in the Browser Window (see Selecting Images to Display) to check alignment between the scanning sequences. Make a note of which scanning sequences are misaligned and use the following instructions to align.

1. Load all locations of one scanning sequence from a patient study. This will be referenced as the base set into Browser #1.

2. Load all locations of another scanning sequence from the same patient study into Browser #2.  This sequence will be registered to the images loaded into Browser #1.

3. In both browsers, select a central location.

4. Using the mouse, get an average value for white matter from each set and calculate a scaling factor = (white matter value browser #1) / (white matter value browser#2).

   Note

   If the scaling factor is around 1, you can skip steps 5 and 6.

5. Select Roi/Voi->Create/Modify from the Main Menu.

   1. Select All Images (2D).

   2. Select Automatic.

      1. Select Fill.

      2. Use left button to select several white matter areas in Browser # 2, then press the right button to get a white matter region encompassing most of the white matter.

   3. Select Roi/Voi Processing.

      1. Press FilG (make sure the Region of Interest/Volume of Interest Dialog has Browser 2 in the title bar, you can pass the mouse over Browser #2 to change it).

         Note

         Check the results by looking at several locations through the image set.  If not satisfactory, clear the values for FilG and repeat steps 5 b and c.

   4. Select Current Image.

   5. Press Cancel to close the Region of Interest/Volume of Interest Dialog.

6. Select Analyze->Miscellaneous->Math.

   1. Enter the scaling factor calculated previously in the 1st Value field.

   2. Press Muk.

      1. Select Browser #2 for Set 1(it should be selected already), with Browser #3 as the Output Browser (it should already be selected, as well).

      2. Press OK.

   3. Press Cancel to close the Math Dialog.

7. Select Analyze->Registration->Register from the Main Window.

   Note

   If you did not perform steps 5 and 6 (normalization) use Browser #2, not Browser #3, for the Reslice Set.

   1. Select AIR for the Match Method.  See the note at the top for important information.

   2. Using the left button over the display image, determine a threshold to include the brain and skin, but not the background for Browser #1 and Browser #3.

      Note

      You can use Threshold in the Region of Interest/Volume of Interest dialog to check the values.

   3. Enter the threshold for Browser #1 in -t1 and the threshold for Browser #3 in -t2.

   4. Press Match.

      1. Select Browser #1 for the Base Set and Browser #3 for the Reslice Set.

      2. Press OK.

   5. Press Reslice.

      1. Select Browser #1 for the Base Set and Browser #2 for the Reslice Set

      2. Press OK.

8. Link Browsers 1, 2, and 4 (set and Send Link as a to Region).

   Note

   If you skipped steps 5 and 6, link Browsers 1, 2, and 3.

   1. Select Automatic, Fill.

      1. Press the left button over white matter in Browser #1, then press the right button several times to completely cover white matter, but not any other anatomy.

   2. Select Morphological.

      1. Press Edgi.

Example Registering using the Mutual Information Method

Warning

The registration process assumes that the 2 sequences being registered have the same slice thickness.  If they do not, click here for instructions on how to  modify the slice thickness of a data set to match another data set.

Load a central location, for all scanning sequences, from a patient study and use the left button in the Browser Window (see Selecting Images to Display) to check alignment between the scanning sequences. Make a note of which scanning sequences are misaligned and use the following instructions to align.

1. Load all locations of one scanning sequence from a patient study. This will be referenced as the base set into Browser #1.

2. Load all locations of another scanning sequence from the same patient study into Browser #2.  This sequence will be registered to the images loaded into Browser #1.

3. In both browsers, select a central location.

4. Select Analyze->Registration->Register from the Main Window.

   1. Select Mutual Information for the Match Method.

   2. Using the left button over the display image, determine a range of values to cover the normal brain anatomy for Browser #1 and Browser #2.

      Note

      You can use Slice in the Region of Interest/Volume of Interest dialog to check the values.

   3. Enter the slice values for Browser #1 in Base and the slice values for Browser #2 in Reslice.

   4. Press Match.

      1. Select Browser #1 for the Base Set and Browser #2 for the Reslice Set.

      2. Press OK.

   5. Press Reslice.

      1. Select Browser #1 for the Base Set and Browser #2 for the Reslice Set

      2. Press OK.

5. Link Browsers 1, 2, and 3 (set and Send Link as a to Region).

   1. Select Automatic, Fill.

      1. Press the left button over white matter in Browser #1, then press the right button several times to completely cover white matter, but not any other anatomy.

   2. Select Morphological.

      1. Press Edgi.

Example Aligning One Image Set

1. Load all locations of one scanning sequence from a patient study.

   Select Contour in the Region of Interest/Volume of Interest Dialog.

   1. Enter 0 for the Lo value.  To select the Hi value: move cursor over the skin area of the image, observe the initial peak in gray level as the skin area is entered (lower-left of the Display Window).  Choose a Hi value slightly less than this peak (~75% of the value).

   2. Use the left button to select an area outside the skin, the upper-right quadrant of the image works best.  This will display the image contour.  Ensure the contour is smooth and free from gross discontinuities, small breaks in the contour and outlines of the nose and ears will not effect the outcome.  Adjust the Hi value as necessary or erase parts of the contour using Erase Irregular and redraw manually using Irregular.

   Note

   Choosing a different point on the image may drastically change the contour outline.

   Ensure, the Region of Interest Dialog displays the Browser # of the images you are working on.  If necessary, move mouse over desired browser and continue working.  This will reset the Browser # of the Region of Interest Dialog.

2. Press Start Macro, select a point outside the skin, press End Macro, and press Run Macro.
   

3. Use the left button in the Browser Window to check all locations for gross errors in the data set.

   1. If any gross errors exist, press another point in the incorrect image to repair. If this does not repair the contour enter a different value for the Hi value and press another point in the incorrect image. (Step 1)

4. Use the right button in the Browser Window to delete any images that do not have sufficient anatomy.

5. Select Rotate if you want to perform rotation when aligning.  Deselect it to translate only.

6. Press Align, each image in turn, will be translated and rotated (if selected).

Example Warping One Image Set to An Expected Image Set

1. Load all locations of one scanning sequence from a patient study. This will be referenced as the expected set into Browser #1.

2. Load all locations of another scanning sequence from the same patient study into Browser #2.  This sequence will be warped to the images loaded into Browser #1.

3. Select 3D in Warp Dimensions.

4. Select Contour in the Region of Interest/Volume of Interest Dialog.

   1. Enter 0 for the Lo value.  To select the Hi value: move cursor over the skin area of the image, observe the initial peak in gray level as the skin area is entered (lower-left of the Display Window).  Choose a Hi value slightly less than this peak (~75% of the value).

   2. Use the left button to select an area outside the skin, the upper-right quadrant of the image works best.  This will display the image contour.  Ensure the contour is smooth and free from gross discontinuities, small breaks in the contour and outlines of the nose and ears will not effect the outcome.  Adjust the Hi value as necessary or erase parts of the contour using Erase Irregular and redraw manually using Irregular.

   Note

   Choosing a different point on the image may drastically change the contour outline.

   Ensure, the Region of Interest Dialog displays the Browser # of the images you are working on.  If necessary, move mouse over desired browser and continue working.  This will reset the Browser # of the Region of Interest Dialog.

5. Press Start Macro, select a point outside the skin, press End Macro, and press Run Macro.
   

6. Use the left button in the Browser Window to check all locations for gross errors between the two sets.

   1. If any gross errors exist, press another point in the incorrect image to repair. If this does not repair the contour enter a different value for the Hi value and press another point in the incorrect image. (Step 3)

7. Use the right button in the Browser Window to delete any images that do not have sufficient anatomy.

   1. Repeat steps 4-7 for the warp images.

8. Press Exp Pts for the expected images (Browser #1) and Wrp Pts for the images to warp (Browser #2).

9. Repeats Steps 6-8 for as many anatomical features you would like to use for calculating the correction table.  You can use any region of interest functions to create the outlines of the anatomical features, as long as you have the outline only (Edgi will create an outline of any solid region of interest).

   Important

   The image border should also be used for one of the features to prevent unexpected results outside the area of interest.  The Invert and Edgi functions in the Region of Interest dialog can be used to create this.

   Note

   You can start over by pressing Clr Exp and Clr Wrp.

   You can display your current expected and warped points by Pressing Dis Exp and Dis Wrp.

10. Select Analyze->Registration->Register from the Main Window.

    1. Press Warp Table. The contours for each set will be saved with "exp" for Browser #1 and "warp" for Browser #2.  Vectors will be drawn on images displaying the direction of warp for each pair of warp -> expected points.  These vectors will also be saved for each image with "warp_to_exp" as the extension.

    2. Press Correct.

Dialog Items

	Match Press Match to determine the translation and rotation parameters to register one set of images to another base set of images.  Select Head/Hat to calculate the translation and rotation parameters using a Head in Hat method.  A contour should be drawn of the same anatomical feature for each set, but does not need to be on all images. Note Both data sets must be the same image size and thickness.  The x and y pixel sizes can be different. Load all images from both sets, although only draw the contours where the anatomical feature exists. A residual value will be printed in the information window indicating the error between the two sets, the lower the value the better.  Press Match repeatedly to improve the residual value, stop when the value increases.  Backup can be pressed to use the prior match with the lower residual value. Select AIR to calculate the translation and rotation parameters using the Automated Image Registration package (alignlinear) from UCLA.  See the note at the top for important information. Enter the threshold value for the Base Set in -t1. Enter the threshold value for the Reslice Set in -t2. Enter the command-line options, including model number,  for alignlinear in Options. -m model_menu_number [options] Model Menu: 3-D models: 6. rigid body 6 parameter model 7. global rescale 7 parameter model 9. traditional 9 parameter model (std must be on AC-PC line) 12. affine 12 parameter model 15. perspective 15 parameter model 2-D models (constrained to in-plane, no interpolation): 23. 2-D rigid body 3 parameter model 24. 2-D global rescale 4 parameter model 25. 2-D affine/fixed determinant 5 parameter model 26. 2-D affine 6 parameter model 28. 2-D perspective 8 parameter model options: (defaults in parentheses) [-b1 FWHM_x(0.000000e+00) FWHM_y(0.000000e+00) FWHM_z(0.000000e+00)] (standard file) [-b2 FWHM_x(0.000000e+00) FWHM_y(0.000000e+00) FWHM_z(0.000000e+00)] (reslice file) [-c convergence_threshold(0.000010)] [-d] use static partitioning (like AIR3.0 and earlier) [-e1 standard_file_mask] [-e2 reslice_file_mask] [-f initialization_file] [-fs scaling_initialization_file] [-g termination_file [overwrite?(y/n)]] [-gs scaling_termination_file [overwrite?(y/n)] [-h halt_after_(5)_iterations_without_improvement] [-j] use non-positive definite Hessian matrices (not validated, use at your own risk) [-p1 segment_standard_file_into_(1)_partitions] [-p2 segment_reslice_file_into_(1)_partitions] [-q] assume non-interaction of spatial parameter derivatives [-r repeated_iterations(25)] [-s initial_sampling(81) final_sampling(1) sampling_decrement_ratio(3)] [-t1 threshold_standard_file(75)] [-t2 threshold_reslice_file(75)] [-v] verbose reporting of interim results [-x cost_function(1)] 1. standard deviation of ratio image 2. least squares 3. least squares with intensity rescaling [-z] (no additional argument; turns on pre-alignment interpolation) Select Mutual Information to calculate the rotation and translation parameters by minimizing the entropy of the intensity plot. (reference) Note This option is currently under development and is not available outside the Henry Ford Health System. Enter the slice values for the Base set in Base, if necessar. Enter the slice values for the Reslice set in Reslice.
	Backup Press Backup to undo the last Match operation (Head/Hat only)
	Reslice Press Reslice to translate and rotate the second image data set to match the first (base) image data set, after performing the Match function. Note The same match results can be used on multiple browsers by pressing Reslice again and selecting the other browser for the Reslice set.  This information is not saved once the user quits the program.
	Align Press Align to align a set of images using contours of an anatomical feature.  The center of mass of each contour is used to translate each image.  The error between each contour is used to determine rotation of each image (first by 10 degrees, 5 degrees, and 1 degree). Rotate option Select Rotate to perform rotation when aligning.  If not selected, only translation will be performed.
	Warp Dimensions Select 2D for single slice processing of warp procedures Select 3D for volume processing of warp procedures.
	Expected Points Press Exp Pts to sample the contour radially around the center and add to the expected points list. Select Rays (2d) to sample warp and expected points by rotating a ray clockwise starting at the top mid-line. Select Rays (3d) to sample warp and expected points by rotating a ray clockwise starting at the top-midline, for each location. Select Edge (2d) to sample warp and expected points by following the contour, starting at the top-midline, and sampling an equal number of points.
	Warp Points Press Warp Pts to sample the contour radially around the center and add to the warp points list.
	Clear Expected Press Clr Exp to clear the expected points list.
	Clear Warp Press Clr Wrp to clear the warp points list.
	Display Expected Press Dis Exp to display the current contents of the expected points list as a region of interest on each image.
	Display Warp Press Dis Wrp to display the current contents of the warp points list as a region of interest on each image.
	Warp Table Press Warp Table to calculate the warp correction tables for the current set of warp and expected points.  The correction is displayed graphically as vector regions of interest on each image connecting the warp point to its corresponding expected point.  The sampled warp and expected points and the correspondence region are automatically saved as region of interest files. Select Bookstein's to calculate the correction tables using Bookstein's method.  This is a look-back method. Select Look-Back to use bi-linear interpolation of the mapping of expected points to warp points to calculate the correction tables. Select Look-Forward to use bi-linear interpolation of the mapping of warp points to expected points to calculate the correction tables.
	Correct Press Correct to correct the selected images using the warp correction tables that were calculated or create images of the X, Y, or Z component of the warp correction tables. Select Look-Back to correct the selected images using a correction table created with a look-back method. Select Look-Forward to correct the selected images using a correction table created with a look-forward method. Select Delta-X to display the X component of the correction table as images. Select Delta-Y to display the Y component of the correction table as images. Select Delta-Z to display the Z component of the correction table as images.
	Cancel Press Cancel to remove the Registration dialog.
	Help Press Help to display help for the Registration dialog.