Open s-kash opened 4 years ago
@jeffduda any chance. you could take a look at this?
This appears to be an ANTs problem that is manifesting in ANTsR. It should just be a one line fix. I can fix it and push it if you want, or would you prefer a PR? Obviously, this fix won't filter up to ANTsR until the ANTs dependency is updated to a version with the fix. Not sure what the current policy is regarding how often the version of ANTs used by ANTsR is updated.
On Thu, Jul 16, 2020 at 7:50 AM stnava notifications@github.com wrote:
@jeffduda https://github.com/jeffduda any chance. you could take a look at this?
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No need for PR.
We are happy to do updates to tags as regularly as needed to fix bugs.
On Thu, Jul 16, 2020 at 5:47 PM Jeffrey Duda notifications@github.com wrote:
This appears to be an ANTs problem that is manifesting in ANTsR. It should just be a one line fix. I can fix it and push it if you want, or would you prefer a PR? Obviously, this fix won't filter up to ANTsR until the ANTs dependency is updated to a version with the fix. Not sure what the current policy is regarding how often the version of ANTs used by ANTsR is updated.
On Thu, Jul 16, 2020 at 7:50 AM stnava notifications@github.com wrote:
@jeffduda https://github.com/jeffduda any chance. you could take a look at this?
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brian
Ok, I pushed the fix to ANTs and all looks good. I don't have push permission for ANTsRCore, but all you need to do is update the configure file with the new ANTs commit tag. I'll put up a PR with that tomorrow if you haven't had a chance to get to that. No changes to ANTsR itself, but it will need to be re-compiled. -jeff
On Thu, Jul 16, 2020 at 5:59 PM stnava notifications@github.com wrote:
No need for PR.
We are happy to do updates to tags as regularly as needed to fix bugs.
On Thu, Jul 16, 2020 at 5:47 PM Jeffrey Duda notifications@github.com wrote:
This appears to be an ANTs problem that is manifesting in ANTsR. It should just be a one line fix. I can fix it and push it if you want, or would you prefer a PR? Obviously, this fix won't filter up to ANTsR until the ANTs dependency is updated to a version with the fix. Not sure what the current policy is regarding how often the version of ANTs used by ANTsR is updated.
On Thu, Jul 16, 2020 at 7:50 AM stnava notifications@github.com wrote:
@jeffduda https://github.com/jeffduda any chance. you could take a look at this?
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brian
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many thanks - yes a PR to antsrcore would be helpful.
brian
On Thu, Jul 16, 2020 at 7:35 PM Jeffrey Duda notifications@github.com wrote:
Ok, I pushed the fix to ANTs and all looks good. I don't have push permission for ANTsRCore, but all you need to do is update the configure file with the new ANTs commit tag. I'll put up a PR with that tomorrow if you haven't had a chance to get to that. No changes to ANTsR itself, but it will need to be re-compiled. -jeff
On Thu, Jul 16, 2020 at 5:59 PM stnava notifications@github.com wrote:
No need for PR.
We are happy to do updates to tags as regularly as needed to fix bugs.
On Thu, Jul 16, 2020 at 5:47 PM Jeffrey Duda notifications@github.com wrote:
This appears to be an ANTs problem that is manifesting in ANTsR. It should just be a one line fix. I can fix it and push it if you want, or would you prefer a PR? Obviously, this fix won't filter up to ANTsR until the ANTs dependency is updated to a version with the fix. Not sure what the current policy is regarding how often the version of ANTs used by ANTsR is updated.
On Thu, Jul 16, 2020 at 7:50 AM stnava notifications@github.com wrote:
@jeffduda https://github.com/jeffduda any chance. you could take a look at this?
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brian
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PR submitted
On Thu, Jul 16, 2020 at 7:40 PM stnava notifications@github.com wrote:
many thanks - yes a PR to antsrcore would be helpful.
brian
On Thu, Jul 16, 2020 at 7:35 PM Jeffrey Duda notifications@github.com wrote:
Ok, I pushed the fix to ANTs and all looks good. I don't have push permission for ANTsRCore, but all you need to do is update the configure file with the new ANTs commit tag. I'll put up a PR with that tomorrow if you haven't had a chance to get to that. No changes to ANTsR itself, but it will need to be re-compiled. -jeff
On Thu, Jul 16, 2020 at 5:59 PM stnava notifications@github.com wrote:
No need for PR.
We are happy to do updates to tags as regularly as needed to fix bugs.
On Thu, Jul 16, 2020 at 5:47 PM Jeffrey Duda <notifications@github.com
wrote:
This appears to be an ANTs problem that is manifesting in ANTsR. It should just be a one line fix. I can fix it and push it if you want, or would you prefer a PR? Obviously, this fix won't filter up to ANTsR until the ANTs dependency is updated to a version with the fix. Not sure what the current policy is regarding how often the version of ANTs used by ANTsR is updated.
On Thu, Jul 16, 2020 at 7:50 AM stnava notifications@github.com wrote:
@jeffduda https://github.com/jeffduda any chance. you could take a look at this?
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brian
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it would be pretty easy to implement the request of returning difference pairs (for relevant methods). That would be an ANTsR update. Should I add that in (in a backwards compatible way) ? -jeff
On Sun, Jul 19, 2020 at 4:09 PM Jeffrey Duda jeff.duda@gmail.com wrote:
PR submitted
On Thu, Jul 16, 2020 at 7:40 PM stnava notifications@github.com wrote:
many thanks - yes a PR to antsrcore would be helpful.
brian
On Thu, Jul 16, 2020 at 7:35 PM Jeffrey Duda notifications@github.com wrote:
Ok, I pushed the fix to ANTs and all looks good. I don't have push permission for ANTsRCore, but all you need to do is update the configure file with the new ANTs commit tag. I'll put up a PR with that tomorrow if you haven't had a chance to get to that. No changes to ANTsR itself, but it will need to be re-compiled. -jeff
On Thu, Jul 16, 2020 at 5:59 PM stnava notifications@github.com wrote:
No need for PR.
We are happy to do updates to tags as regularly as needed to fix bugs.
On Thu, Jul 16, 2020 at 5:47 PM Jeffrey Duda < notifications@github.com> wrote:
This appears to be an ANTs problem that is manifesting in ANTsR. It should just be a one line fix. I can fix it and push it if you want, or would you prefer a PR? Obviously, this fix won't filter up to ANTsR until the ANTs dependency is updated to a version with the fix. Not sure what the current policy is regarding how often the version of ANTs used by ANTsR is updated.
On Thu, Jul 16, 2020 at 7:50 AM stnava notifications@github.com wrote:
@jeffduda https://github.com/jeffduda any chance. you could take a look at this?
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brian
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that sounds good - I just tested the surround subtract and it worked in the sense that it did not crash. will try some time later this month on real data.
Hi ANTsR team,
Describe the bug I'm trying the ASL processing tools available in ANTsR. Particularly to obtain pair-wise differences of a timeseries. I want to compare the different perfusion subtraction methods available. However, all four: "simpleSubtract","surroundSubtract","cubicSubtract" and ""sincSubtract" all crash with the following error message (example for one method):
ITK ExceptionObject caught! Error in aslAveraging(input_asl, mask = NULL, method = "surroundSubtract") : /usr/local/lib/R/site-library/ITKR/libs/include/ITK-5.1/itkImageSource.hxx:268: itk::ERROR: AverageOverDimensionImageFilter(0x563b5e72cf10): Subclass should override this method!!! If old behavior is desired invoke this->DynamicMultiThreadingOff(); before Update() is called. The best place is in class constructor.
To Reproduce Steps to reproduce the behavior: input_asl <- antsImageRead("test_asl_timeseries.nii.gz") perf_asl_surrsub <- aslAveraging(input_asl, mask = NULL, method = "surroundSubtract")
Expected behavior I expect the command to provide the temporal mean of the pair-wise difference of the ASL time-series. Isn't this right? Although, I'd prefer it give me the entire pair-wise difference time-series (before averaging) as well.
Desktop (please complete the following information):
Additional context Rstudio v 1.2.5001 and R version 3.6.3
Help is appreciated.
Thanks, Sri