How to pass command line arguments to antsRegistration?

[muratmaga]

If I set the printArgs to TRUE, I can see the full set of antsRegistration parameters.

 mytx2 <- antsRegistration(fixed=fi,  moving=mi, typeofTransform = 'SyN', printArgs = TRUE)
antsRegistration -d 2 -r [0x56123776d170,0x56123c7e44e0,1] -m mattes[0x56123776d170,0x56123c7e44e0,1,32,regular,0.2] -t Affine[0.25] -c 2100x1200x1200x0 -s 3x2x1x0 -f 4x2x2x1 -x [NA,NA] -m mattes[0x56123776d170,0x56123c7e44e0,1,32] -t SyN[0.2,3,0] -c [ 40x20x0 ,1e-7,8] -s 2x1x0 -f 4x2x1 -u 0 -z 1 -o [/tmp/RtmpP0uvUG/file33d6b650120ba,0x56123652cab0,0x56123c317c70] -x [NA,NA] --float 1 --random-seed 1 --write-composite-transform 0 

I want to use this to modify some of the settings that are not exposed by R call. However, I couldn't figure out how to pass this back to antsRegistration. Documentation shows an example, but the call fails since it points to a file on disk, as opposed to an array in memory.

 antsRegistration( list( d=2,m="mi[r16slice.nii.gz,r64slice.nii.gz,1,20,Regular,0.05]", t="affine[1.0]", c="2100x1200x1200x0",  s="3x2x1x0", f="4x3x2x1", u="1", o="[xtest,xtest.nii.gz,xtest_inv.nii.gz]" ) )```

[ncullen93]

You'll have to look through the antsRegistration code in ANTsR and ANTsRCore probably more specifically, because I don't believe there is a way to add any additional parameters. Happy to accept a PR if you think something is missing... it should be easy to just add the function argument to antsRegistration and then add that arg to the parameters that are built up.

[cookpa]

I've not used the list option but I believe you would need to replace file names with pointers to antsImage objects using antsrGetPointerName, eg

img_pt <- antsrGetPointerName( antsImageClone( img ))

I include the clone here from the man example, the antsRegistration function also clones the input image.

[muratmaga]

@cookpa Thanks for the pointer info. However, if I do antsImageClone, the pointer address changes every time. Is there reason antsr is not directly using the actual address of the image?

> fi <- antsImageRead(getANTsRData("r16") )
> mi <- antsImageRead(getANTsRData("r64") )
> 
> antsrGetPointerName(fi)
[1] "0x561b9ba33b30"
> antsrGetPointerName(mi)
[1] "0x561b9bd504e0"
> 
> 
> mytx2 <- antsRegistration(fi,  mi, typeofTransform = 'Affine', printArgs = T)
antsRegistration -d 2 -r [0x561b9c78e900,0x561b9c7cec50,1] -m mattes[0x561b9c78e900,0x561b9c7cec50,1,32,regular,0.2] -t Affine[0.25] -c 2100x1200x1200x10 -s 3x2x1x0 -f 6x4x2x1 -u 0 -z 1 -o [/tmp/Rtmp01coMb/file118bd916264147,0x561b9bd30860,0x561b98aece90] -x [NA,NA] --float 1 --random-seed 1 --write-composite-transform 0 
> antsrGetPointerName(antsImageClone(fi))
[1] "0x561b9bc6f0c0"
> antsrGetPointerName(antsImageClone(fi))
[1] "0x561b9bed7170"

clearly antsRegistration is using the antsImageClone too, since every call has a different pointer address. So not sure how to do convert this a list call

> mytx2 <- antsRegistration(fi,  mi, typeofTransform = 'Affine', printArgs = T)
antsRegistration -d 2 -r [0x561b9ba32fd0,0x561b9bac0570,1] -m mattes[0x561b9ba32fd0,0x561b9bac0570,1,32,regular,0.2] -t Affine[0.25] -c 2100x1200x1200x10 -s 3x2x1x0 -f 6x4x2x1 -u 0 -z 1 -o [/tmp/Rtmp01coMb/file118bd91a9f7941,0x561b9f72e800,0x561b9bc68ab0] -x [NA,NA] --float 1 --random-seed 1 --write-composite-transform 0 
> mytx2 <- antsRegistration(fi,  mi, typeofTransform = 'Affine', printArgs = T)
antsRegistration -d 2 -r [0x561b9bc68fc0,0x561b9cbdb9c0,1] -m mattes[0x561b9bc68fc0,0x561b9cbdb9c0,1,32,regular,0.2] -t Affine[0.25] -c 2100x1200x1200x10 -s 3x2x1x0 -f 6x4x2x1 -u 0 -z 1 -o [/tmp/Rtmp01coMb/file118bd96a38f2d9,0x561b9c6a47c0,0x561b9bd303f0] -x [NA,NA] --float 1 --random-seed 1 --write-composite-transform 0 

[cookpa]

Yes you'd get another pointer each time, they are pointers to copies of the image. Sorry, the example I gave was probably not very useful. To avoid garbage collection you'd need to keep a reference around, so something like

fi_for_reg = antsImageClone(fi) mi_for_reg = antsImageClone(mi)

Then in your antsRegistration parameter list, you'd replace the file names with antsrGetPointerName(fi_for_reg) and antsrGetPointerName(mi_for_reg)

I don't actually know why antsRegistration clones the input images this way, but it does.