Closed ntustison closed 4 years ago
Hey @stnava , this is the only commit I need before we can process the perfusion data. It's basically just a couple lines to process a single data set:
perfusionImage <- antsImageRead( perfusionFile )
voiMaskImage <- antsImageRead( brainMaskFile )
perfusion <- bloodPerfusionSVD( perfusionImage, voiMaskImage, thresholdSVD = 0.2, deltaTime = 1.0 )
antsImageWrite( perfusion$cbfImage, "cbfImage.nii.gz" )
antsImageWrite( perfusion$cbvImage, "cbvImage.nii.gz" )
antsImageWrite( perfusion$mttImage, "mttImage.nii.gz" )
but I've also added some visualization capabilities which I'll demonstrate in the example I'll send you after this gets merged.
Weird - seeing failures on https://travis-ci.org/muschellij2/ANTsR/jobs/642453185#L10273 and https://travis-ci.org/ANTsX/ANTsR/jobs/641895019#L10206
@muschellij2 Yeah, thanks for taking a look. I'm at a loss as to why those failures are occurring with this pull request.
sorry - I am stretched pretty thin til something like the 6th of February but might be able to look closer this upcoming weekend.
brian
On Mon, Jan 27, 2020 at 1:57 PM Nick Tustison notifications@github.com wrote:
@muschellij2 https://github.com/muschellij2 Yeah, thanks for taking a look. I'm at a loss as to why those failures are occurring with this pull request.
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@stnava --- No urgency as I just pulled this branch to the local machine for processing the breacher data. Whenever you can is fine.
Previously, the function
bloodPerfusionSVD
required an arterial input function (AIF) mask image to generate the CBF, etc. images. This commit adds the ability to automatically generate a mask using this approach.