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  • Posted a comment on discussion Help on Advanced Normalization Tools ( ANTs )

    yes - or you can create a "flipping" transform and just apply it. antsr (and probably antspy) has functionality for this. brian On Fri, Oct 6, 2017 at 5:27 PM, Nick Tustison ntustison@users.sf.net wrote: Yeah, anything beyond a 30 degree discrepancy between fixed and moving objects is going to be difficult to capture using the traditional image registration approach. One option is to use the antsLandmarkBasedTransformInitializer with corresponding template and T1-weighted landmarks to get a rough...

  • Posted a comment on discussion Help on Advanced Normalization Tools ( ANTs )

    Do you have a recent version of ants downloaded from github? On Fri, Sep 8, 2017 at 12:45 PM Jason Smith smithjf@users.sf.net wrote: Hello, I am getting segmentation errors using antsMotionCorr but only occasionally (i.e. I can type the same exact command 4 times, have it dump with different durations 3 times and succeed on the 4th). I can run stack traces if needed. the exact command is below in case I have errors in the actual call. Thanks j antsMotionCorr -d 3 -o [ ${dataDir}/radoACI001_07_ep2d_N110,...

  • Posted a comment on discussion Open Discussion on Advanced Normalization Tools ( ANTs )

    Set -v 1 to get verbose output Also, pass Warp.nii.gz not Warped.nii.gz To -t option On Mon, Sep 4, 2017 at 12:10 AM Abdur Raquib Ridwan ridwan34shila@users.sf.net wrote: I have exactly the same issue and even when I try to convert the mat file to .txt using ConvertTransformFile, it fails. I can't figure out the reason, and I also tried changing the name to simple name like baby.mat but still fails. antsApplyTransforms help https://sourceforge.net/p/advants/discussion/840260/thread/386c6f69/?limit=25#3aa0...

  • Posted a comment on discussion Help on Advanced Normalization Tools ( ANTs )

    Antsr Provides this. On Sun, Sep 3, 2017 at 6:51 PM Nick Tustison ntustison@users.sf.net wrote: I don't believe we have a function that calculates the median value within a mask although it should be pretty easy to create one. ANTS - get median within mask region https://sourceforge.net/p/advants/discussion/840261/thread/30bf4279/?limit=25#22d5/8ca0 Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/advants/discussion/840261/ To unsubscribe from further messages,...

  • Posted a comment on discussion Help on Advanced Normalization Tools ( ANTs )

    The algorithm is a gradient descent method. What do you propose is like reducing the step size in GD. For your second question, the Laplacian undoes the blurring induced by averaging. Therefore, it produces an image that is more like a realistic brain image On Thu, Aug 10, 2017 at 6:19 PM Abdur Raquib Ridwan ridwan34shila@users.sf.net wrote: Dear Nick, I have read the paper https://www.ncbi.nlm.nih.gov/pubmed/19818860 like you told me to. So if I am not wrong is the final step where the warpfield...

  • Posted a comment on discussion Help on Advanced Normalization Tools ( ANTs )

    you would need to share the original antsRegistration call to get meaningful help brian On Thu, Aug 10, 2017 at 8:58 AM, Paul Glad Mihai gladomat@users.sf.net wrote: Hi there, I computed the composite transform through antsRegistration but don't have an image named inverse.nii.gz . When I try to apply an inverse transform with only the .h5 file it complains that the inverse does not exist for this file. Is there a way to compute the inverse from the forward transform? Does something like this make...

  • Posted a comment on discussion Help on Advanced Normalization Tools ( ANTs )

    you can skip the last level by doing: --shrink-factors 10x6x4x2 --smoothing-sigmas 5x3x2x1vox --convergence [100x100x70x50,1e-6,10] brian On Wed, Aug 9, 2017 at 11:35 AM, Tilo xtwi001@users.sf.net wrote: We used: antsRegistration --verbose 1 --dimensionality 3 --float 1 --collapse-output-transforms 1 --output [CT_Reg_,CT_Reg_Warped.nii.gz, CT_Reg_InverseWarped.nii.gz] --interpolation Linear --use-histogram-matching 1 --winsorize-image-intensities [0.005,0.995] --initial-moving-transform [CT_fixed.mha,CT_moving.mha,1]...

  • Posted a comment on discussion Open Discussion on Advanced Normalization Tools ( ANTs )

    Yes - probably MRtrix brian On Sun, Aug 6, 2017 at 11:10 AM, sandro romanzetti sroman11@users.sf.net wrote: Hi everyone, I would be grateful if anyone would give me any reccomendation for a diffusion toolbox. I read in the documentation/discussions/helps that Camino once was the preffered choice, but since this is not maintained anymore, MRtrix would be the next best package to use alongside ANTs/ANTsR. Many thanks in advance Sandro Diffusion toolbox https://sourceforge.net/p/advants/discussion/840260/thread/a7b9bada/?limit=25#2b50...

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