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Subtraction methods fail in aslAveraging #319
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@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 ***@***.***> 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 ***@***.***> wrote:
> @jeffduda <https://github.com/jeffduda> any chance. you could take a
look
> at this?
>
> —
> You are receiving this because you were mentioned.
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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 ***@***.***> 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 ***@***.***>
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 ***@***.***> wrote:
>
> > @jeffduda <https://github.com/jeffduda> any chance. you could take a
> look
> > at this?
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#319 (comment)>, or
> > unsubscribe
> > <
>
https://github.com/notifications/unsubscribe-auth/AAD5NCFD6TUTQMW4RMPUQMTR33SPDANCNFSM4NMPEKJA
> >
> > .
> >
>
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> You are receiving this because you commented.
>
>
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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 ***@***.***> 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 ***@***.***>
> 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 ***@***.***>
wrote:
> >
> > > @jeffduda <https://github.com/jeffduda> any chance. you could take a
> > look
> > > at this?
> > >
> > > —
> > > You are receiving this because you were mentioned.
> > > Reply to this email directly, view it on GitHub
> > > <#319 (comment)>,
or
> > > unsubscribe
> > > <
> >
>
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> > >
> > > .
> > >
> >
> > —
> > You are receiving this because you commented.
> >
> >
> > Reply to this email directly, view it on GitHub
> > <#319 (comment)>, or
> > unsubscribe
> > <
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> >
> > .
> >
> --
>
> brian
>
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PR submitted
…On Thu, Jul 16, 2020 at 7:40 PM stnava ***@***.***> wrote:
many thanks - yes a PR to antsrcore would be helpful.
brian
On Thu, Jul 16, 2020 at 7:35 PM Jeffrey Duda ***@***.***>
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 ***@***.***> 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 ***@***.***
>
> > 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 ***@***.***>
> wrote:
> > >
> > > > @jeffduda <https://github.com/jeffduda> any chance. you could
take a
> > > look
> > > > at this?
> > > >
> > > > —
> > > > You are receiving this because you were mentioned.
> > > > Reply to this email directly, view it on GitHub
> > > > <#319 (comment)
>,
> or
> > > > unsubscribe
> > > > <
> > >
> >
>
https://github.com/notifications/unsubscribe-auth/AAD5NCFD6TUTQMW4RMPUQMTR33SPDANCNFSM4NMPEKJA
> > > >
> > > > .
> > > >
> > >
> > > —
> > > You are receiving this because you commented.
> > >
> > >
> > > Reply to this email directly, view it on GitHub
> > > <#319 (comment)>,
or
> > > unsubscribe
> > > <
> >
>
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> > >
> > > .
> > >
> > --
> >
> > brian
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
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> > <
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> >
> > .
> >
>
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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 ***@***.***> wrote:
PR submitted
On Thu, Jul 16, 2020 at 7:40 PM stnava ***@***.***> wrote:
> many thanks - yes a PR to antsrcore would be helpful.
>
> brian
>
>
>
> On Thu, Jul 16, 2020 at 7:35 PM Jeffrey Duda ***@***.***>
> 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 ***@***.***>
> 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 <
> ***@***.***>
> > > 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 ***@***.***>
> > wrote:
> > > >
> > > > > @jeffduda <https://github.com/jeffduda> any chance. you could
> take a
> > > > look
> > > > > at this?
> > > > >
> > > > > —
> > > > > You are receiving this because you were mentioned.
> > > > > Reply to this email directly, view it on GitHub
> > > > > <#319 (comment)
> >,
> > or
> > > > > unsubscribe
> > > > > <
> > > >
> > >
> >
> https://github.com/notifications/unsubscribe-auth/AAD5NCFD6TUTQMW4RMPUQMTR33SPDANCNFSM4NMPEKJA
> > > > >
> > > > > .
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> > > >
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> > > >
> > > >
> > > > Reply to this email directly, view it on GitHub
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> > >
> >
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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. |
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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
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