Seth Ryan

Hello ANTs experts, I have a linear transformation file (translation + rotation) in Dicom format (Modality tagged as REG in header) and I want to either convert this to any of mat/tfm/nifti/nrrd/mha etc. format or directly apply it to an image using antsApplyTransforms. I tried the latter but didn't work. I also tried to conver it using ITK Dicom to nifti code but it doesn't seem to be designed for a REG transformation as it only supports GDCMImageIO. Is this possible somehow? Thanks, Seth

Thanks. One last question: In the docs, I see ANTs uses ITK histogram matching filter "itk::HistogramMatchingImageFilter". Is ThresholdAtMeanIntensityOn() switched on by default?

Hi Nick, I looked at the algorithm used for Histogram matching and I have a question: Does it make sense to use HistogramMatching when doing a multi-modality registration like MR-CT registration or they should be at least the same modality with probably different intensity distribution? e.g. Contrast and non-contrast CT. Because I guess MR and CT have different intensity distribution and try matching some points in their histogram of the entire image maybe doesn't do anything useful? I'm not sure...

Great! Thanks Nick. One final thing, is there any ANTs paper that mentions this issue?

Thanks, Nick. I used Mattes mutual information metric actually, because that was less sensitive to different parameters and I got much better registration results. It is also faster than CC. Does Mattes require rescaling?

Btw, I do the histogram matching, though.

Hello ANTs experts, I am doing 2 types of registerations using BSyN i.e. MRI to CT multimodality and MRI to MRI monomodality. The MRI images are weekly scans (5 scans). All the MRI images have more or less the same intensity distribution 0~500/600 (Min~Max). I was wondering if I have to standardize/normalize all the MRI images before doing the registrations? What I asume is that since registration itself is kind of a normalization task (minimize the intensity difference) and tries to normalize the...

Hello ANTs folks, I was wondering what's the default value for out of frame regions in antsRegistrationSyNQuick? Is there somewhere I can change the value? I didn't find it in -h. Thanks, Seth