antsApplyTrsnforms inside R

[Arman]

Hi,

I'm having trouble passing two files (one affine transformation and one
warp file) to ANTsR to apply serial transformations, my command is:

outimg <- antsApplyTransforms( fixed=t1 , moving=t2 ,
transformlist=list("path/to/file.mat",
"/path/to/file/file-reg1Warp.nii.gz"))

The error that I get is:

Error in file.exists(transformlist[i]) : invalid 'file' argument

However outside of R the above files work good with antsApplyTransforms.
Any input is greatly appreciated.

All the best,
Arman

[stnava]

here is an example from ?antsRegistration

fi<-antsImageRead( getANTsRData('r16') ,2)
mi<-antsImageRead( getANTsRData('r64') ,2)
mytx<-antsRegistration(fixed=fi , moving=mi , typeofTransform =
c("SyN"), outprefix=paste(tempdir(),"/Z",sep=''))

mywarpedimage<-antsApplyTransforms(fixed=fi,moving=mi,transformlist=mytx$fwdtransforms)

what is different about your case and this one?

this one works fine .... here is the representation:

mytx$fwdtransforms
[1]
"/var/folders/jc/_ktt55mn2ddcd8bcf88jrf0h0000gn/T//RtmpqFUVbB/Z1Warp.nii.gz"

[2]
"/var/folders/jc/_ktt55mn2ddcd8bcf88jrf0h0000gn/T//RtmpqFUVbB/Z0GenericAffine.mat"

typeof(mytx$fwdtransforms)
[1] "character"
mytx$fwdtransforms[[1]]
[1]
"/var/folders/jc/_ktt55mn2ddcd8bcf88jrf0h0000gn/T//RtmpqFUVbB/Z1Warp.nii.gz"
mytx$fwdtransforms[[2]]
[1]
"/var/folders/jc/_ktt55mn2ddcd8bcf88jrf0h0000gn/T//RtmpqFUVbB/Z0GenericAffine.mat"

brian

On Sat, Nov 9, 2013 at 9:19 AM, Arman armaneshaghi@users.sf.net wrote:

Hi,

I'm having trouble passing two files (one affine transformation and one
warp file) to ANTsR to apply serial transformations, my command is:

outimg <- antsApplyTransforms( fixed=t1 , moving=t2 ,
transformlist=list("path/to/file.mat",
"/path/to/file/file-reg1Warp.nii.gz"))

The error that I get is:

Error in file.exists(transformlist[i]) : invalid 'file' argument

However outside of R the above files work good with antsApplyTransforms.
Any input is greatly appreciated.

All the best,
Arman

---

antsApplyTrsnforms inside Rhttp://sourceforge.net/p/advants/discussion/840261/thread/1187f990/?limit=25#e7be

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[Arman]

Thanks Brian! I was a bit ignorant

Sent from a mobile device, please excuse my brevity/misspellings.

On Nov 9, 2013, at 6:48 PM, "stnava" stnava@users.sf.net wrote:

here is an example from ?antsRegistration

fi<-antsImageRead( getANTsRData('r16') ,2)
mi<-antsImageRead( getANTsRData('r64') ,2)
mytx<-antsRegistration(fixed=fi , moving=mi , typeofTransform =
c("SyN"), outprefix=paste(tempdir(),"/Z",sep=''))

mywarpedimage<-antsApplyTransforms(fixed=fi,moving=mi,transformlist=mytx$fwdtransforms)

what is different about your case and this one?

this one works fine .... here is the representation:

mytx$fwdtransforms
[1]
"/var/folders/jc/_ktt55mn2ddcd8bcf88jrf0h0000gn/T//RtmpqFUVbB/Z1Warp.nii.gz"

[2]
"/var/folders/jc/_ktt55mn2ddcd8bcf88jrf0h0000gn/T//RtmpqFUVbB/Z0GenericAffine.mat"

typeof(mytx$fwdtransforms)
[1] "character"
mytx$fwdtransforms[[1]]
[1]
"/var/folders/jc/_ktt55mn2ddcd8bcf88jrf0h0000gn/T//RtmpqFUVbB/Z1Warp.nii.gz"
mytx$fwdtransforms[[2]]
[1]
"/var/folders/jc/_ktt55mn2ddcd8bcf88jrf0h0000gn/T//RtmpqFUVbB/Z0GenericAffine.mat"

brian

On Sat, Nov 9, 2013 at 9:19 AM, Arman armaneshaghi@users.sf.net wrote:

Hi,

I'm having trouble passing two files (one affine transformation and one
warp file) to ANTsR to apply serial transformations, my command is:

outimg <- antsApplyTransforms( fixed=t1 , moving=t2 ,
transformlist=list("path/to/file.mat",
"/path/to/file/file-reg1Warp.nii.gz"))

The error that I get is:

Error in file.exists(transformlist[i]) : invalid 'file' argument

However outside of R the above files work good with antsApplyTransforms.
Any input is greatly appreciated.

All the best,
Arman

antsApplyTrsnforms inside Rhttp://sourceforge.net/p/advants/discussion/840261/thread/1187f990/?limit=25#e7be

Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/advants/discussion/840261/

To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/

antsApplyTrsnforms inside R

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[Bryson Reynolds]

Ok, so I had this same problem. This thread slightly helped, but I want to make explicit what helped me fix the problem
In R, when you run:
antsApplyTransforms()
it provides the example
warpedimg<-antsApplyTransforms( fixed=img1 , moving=img2 , transformlist=list("my0GenericAffine.mat","my1Warp.nii.gz") )
But, when I use list() to create the transformlist I get that error.
Error in file.exists(transformlist[i]) : invalid 'file' argument
FYI,
translist=list("my0GenericAffine.mat","my1Warp.nii.gz") typeof(translist) [1] "list")

However, when I create the transform list this way:
translist<-"my1Warp.nii.gz" translist[2]<-"my0GenericAffine.mat"
FYI
typeof(translist) [1] "character"
and call
warpedimg<-antsApplyTransforms(fixed=img1, moving=img2, transformlist=translist)
it works fine.

Hope that helps someone else.