stnava
commented
6 years ago Just upload heavily downsampled versions. The images define the reference spaces etc. so are needed to understand the issue.
On Wed, Mar 14, 2018 at 1:55 AM muratmaga notifications@github.com wrote:
Hi all,
Sorry to bother y'all with this. But I am utterly confused. There is a volume on which I did collected landmarks in Slicer (original.fcsv). I rigidly registered this volume to a reference in AntsR using the antsRegistration and saved the resultant affine fwdtransform (tranform.mat) as well as the warped moving image.
If I import the original.fcsv and apply the affine transform in slicer to it, everything lines up (final.fcsv) correctly with respect to the transformed image. But I want to do this programmatically in AntsR. This is what I tried with the antsApplyTransformsToPoints
lms=Morpho::read.fcsv('original.fcsv') transform='transform.mat' lms=t(t(lms) * c(-1, -1, 1)) #this is for RAS2LPS conversion.
setting the whichtoinvert to T or F makes no difference below
new.pts=antsApplyTransformsToPoints(dim = 3, points = lms, transformlist = transform)
new.pts[1:5,] Morpho::read.fcsv('final.fcsv')[1:5,]
obviously they are not the same. Can someone show me the correct way of doing this?
I attached the original landmark set, the affine transform I am trying to apply and what the coordinates should be after if the transformation is correctly applied. Images are too big to attach, but can upload somewhere else, and if they are useful.
files.zip https://github.com/ANTsX/ANTsR/files/1809738/files.zip
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/207, or mute the thread https://github.com/notifications/unsubscribe-auth/AATyfs8y9YnIxExsfd_L1rA76orHcM0Aks5teLDNgaJpZM4Sp4Hf .
--
brian
muratmaga
Hi all,
Sorry to bother y'all with this. But I am utterly confused. There is a volume on which I did collected landmarks in Slicer (original.fcsv). I rigidly registered this volume to a reference in AntsR using the antsRegistration and saved the resultant affine fwdtransform (tranform.mat) as well as the warped moving image.
If I import the original.fcsv and apply the affine transform in slicer to it, everything lines up (final.fcsv) correctly with respect to the transformed image. But I want to do this programmatically in AntsR. This is what I tried with the antsApplyTransformsToPoints
lms=Morpho::read.fcsv('original.fcsv') transform='transform.mat' lms=t(t(lms) * c(-1, -1, 1)) #this is for RAS2LPS conversion.
setting the whichtoinvert to T or F makes no difference below
new.pts=antsApplyTransformsToPoints(dim = 3, points = lms, transformlist = transform)
new.pts[1:5,] Morpho::read.fcsv('final.fcsv')[1:5,]
obviously they are not the same. Can someone show me the correct way of doing this?
I attached the original landmark set, the affine transform I am trying to apply and what the coordinates should be after if the transformation is correctly applied. Images are too big to attach, but can upload somewhere else, and if they are useful.
files.zip