search

nipy / nipype

Workflows and interfaces for neuroimaging packages
https://nipype.readthedocs.org/en/latest/
Other
751 stars 530 forks source link

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

Open oesteban opened 10 years ago

oesteban commented 10 years ago

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 commented 10 years ago

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 commented 10 years ago

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.

akeshavan commented 5 years ago

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: https://github.com/nipy/nipype/pull/2832

nqueder commented 2 years ago

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 commented 11 months ago

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?

tasciseda commented 4 months ago

How did you add slice to your image? Thank you.