How to conduct the inverse of '3dWarp -oblique2card'?

AFNI Message Board
1

Hi AFNI experts,
The anatomy dataset had been deobliqued using 3dWarp for each subject firstly:


3dWarp -oblique2card -prefix card OriginalAnatomy+orig.

And then many ROIs were drawn on card+orig.
Now I want to transform these cardinal ROIs back to match the original oblique dataset (OriginalAnatomy+orig) perfectly.
And I have tried the method like this:


3dWarp -card2oblique OriginalAnatomy+orig. -prefix reoblique card+orig.

But it doesn’t work because the afni GUI said there is still oblique angle difference of 2.97 degrees between reoblique+orig. and OriginalAnatomy+orig.
Do you know how to process the ROIs to make them match the original oblique dataset perfectly?
I’m very sorry to disturb you.
Best regards,
Yu

2

Use the -gridset option to force the grid to the original dataset and use 3drefit to copy the IJK_TO_DICOM_REAL attribute from the original dataset to the output dataset You can see the xyz->xyz transformation matrix used with the “-verb” option and invert that with cat_matvec.

3

Hi Daniel,
Thank you!
I seem to have found an easy way to do the inversion:
As mentioned before, I got the deobliqued dataset using the code:


[size=small]3dWarp -oblique2card -prefix card OriginalAnatomy+orig.[/size]

When I open the card+orig.HEAD file now, I find two new attributes that are different from the attributes in OriginalAnatomy+orig.HEAD:


 [size=small]type  = float-attribute
name  = WARPDRIVE_MATVEC_FOR_000000
count = 12
      0.9955035    -0.03815642     0.08670011       1.430454     0.05067991
      0.9878103     -0.1471824      -17.53901     -0.0800273      0.1509146
      0.9853023       28.11709
type  = float-attribute
name  = WARPDRIVE_MATVEC_INV_000000
count = 12
      0.9955035     0.05067991     -0.0800273       1.714989    -0.03815642
      0.9878101      0.1509145       13.13652     0.08670011     -0.1471824
      0.9853022      -30.40928[/size]

I think WARPDRIVE_MATVEC_INV_000000 is the attribute of inversion matrix.
And I can transform card+orig back to match OriginalAnatomy+orig using these codes:


[size=small]cat_matvec card+orig::WARPDRIVE_MATVEC_INV_000000 > inverion.1D
3dAllineate -1Dmatrix_apply inversion.1D -prefix reoblique+orig -source card+orig -master OriginalAnatomy+orig[/size]

Unfortunately, the afni GUI say reoblique+orig and OriginalAnatomy+orig still have an angle difference of 9.835 degrees.
This warning makes me very sad !! :-(:frowning:
So I compare the matrix outputted by 3dWarp -verb and the matrix stored in card+orig.HEAD for checking:


[size=small]3dWarp -verb -oblique2card -prefix card OriginalAnatomy+orig. >forward_verb.1D
cat_matvec -ONELINE forward_verb.1D
     0.995503   0.05068  -0.080027   1.71499   -0.038156   0.98781   0.150915    13.1365    0.0867   -0.147182  0.985302   -30.4093
cat_matvec -ONELINE card+orig::WARPDRIVE_MATVEC_FOR_000000
    0.995503   -0.0381564    0.0867001     1.43045   0.0506799    0.98781   -0.147182    -17.539   -0.0800273     0.150915    0.985302    28.1171
cat_matvec -ONELINE card+orig::WARPDRIVE_MATVEC_INV_000000
    0.995503    0.0506799    -0.0800273       1.71499    -0.0381564     0.98781    0.150915   13.1365    0.0867001    -0.147182     0.985302    -30.4093[/size]

This makes me very confused! :-S:-S
Because I thought the matrix outputted by 3dWarp -verb is the forward matrix. It is unexpectedly the same as the inversion matrix stored in the HEAD file now.
What do you think?
Yu

4

You need to use 3drefit to modify the header of the reoblique dataset to include the same “IJK_TO_DICCOM_REAL” attribute of the original dataset.

5

I am very sorry for so many questions. But now I have only the last two questions to verify:

  1. The inverse matrix, NOT the forward matrix is outputted to the terminal by 3dWarp -verb?
  2. I can change the deobliqued dataset to match the original dataset perfectly using the following codes?

#3dWarp -oblique2card -prefix card OriginalAnatomy+orig.
cat_matvec -ONELINE card+orig::WARPDRIVE_MATVEC_INV_000000 > inversion.1D
3dAllineate -1Dmatrix_apply inversion.1D -prefix reoblique+orig -source card+orig -master OriginalAnatomy+orig
3drefit -atrcopy OriginalAnatomy+orig. IJK_TO_DICOM_REAL reoblique+orig

Am I right about these two questions?
Best regards,
Yu

6

It’s best to check this out with obviously oblique data. I just tried your example, and this works!

7

Hi Daniel,
At the last step of inverse processing, we copied the attribute IJK_TO_DICOM_REAL from the original dataset to the reobliqued dataset using:


3drefit -atrcopy OriginalAnatomy+orig. IJK_TO_DICOM_REAL reoblique+orig

And the Afni GUI didn’t give an angle difference warning anymore.

But just now, I find the help files of 3drefit say the option -atrcopy can’t really change an attribute without the option -saveatr ?
I am very confused.
Maybe I should do the last step using:


3drefit -saveatr -atrcopy OriginalAnatomy+orig. IJK_TO_DICOM_REAL reoblique+orig

Which is the right one?
With anticipation,
Yu

8

While “-saveatr” won’t hurt, it isn’t necessary for this kind of dataset attribute. The atrcopy is good enough here.