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TOPUP and ApplyTOPUP crash with images with odd number of pixels #948

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oesteban opened this issue Oct 10, 2014 · 5 comments · May be fixed by #2832
Open

TOPUP and ApplyTOPUP crash with images with odd number of pixels #948

oesteban opened this issue Oct 10, 2014 · 5 comments · May be fixed by #2832

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@oesteban
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When any of the dimensions of the images has odd number of pixels, topup crashes:

Topup: msg=topup_clp::topup_clp: Subsampling levels incompatible with image data

It'd be great if the interfaces checked this and transparently added the slices as FSL experts suggest here: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;67dcb45c.1209
@satra
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satra commented Oct 10, 2014

instead of adding we could subtract, but this will depend on the field of view of the data. if that is tight one could run into issues. i think we leave this to the user. we could make a note of this in the docstrings of topup and applytopup

@oesteban
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Yes, it's better to subtract. Anyways, I need this in my pipelines, so I will have the implementation in my fork. Just in case we reconsider leaving this to the user, it's only a PR.

oesteban added a commit to oesteban/nipype that referenced this issue Oct 10, 2014
@oesteban
Topup inputs check. Close nipy#948
4616c73
@akeshavan akeshavan linked a pull request Dec 19, 2018 that will close this issue
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@akeshavan
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akeshavan commented Dec 19, 2018 •
edited

I'm reopening this! I'm still having this problem. I've changed oscar's original commit by adding a flag to turn the resizing on/off.

For some reason, the applytopup interface isn't working. Any ideas? Here's the PR: #2832

@akeshavan akeshavan reopened this Dec 19, 2018
@nqueder
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nqueder commented Apr 19, 2022

I noticed that this issue is a bit old, but I am running into the same error when I'm trying to run topup on my dmri dataset.
Has anyone been able to find a way around it?

@DISAPPEARED13
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DISAPPEARED13 commented Dec 18, 2023 •
edited

I solved this problem with adding some slices in the front and back of the volume... I thought that my data got something wrong or I gave the wrong input, but is it very common for adding slices to solve this kind of problem?

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Enh/wip/fix/brk topup for odd dimensions. help needed akeshavan/nipype
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@satra @oesteban @akeshavan @nqueder @DISAPPEARED13