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CBICA / HistoReg

Framework for registration of sequential digitized histology slices
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Segmentation fault #4

Closed phiwei closed 4 years ago

phiwei commented 4 years ago

Hi,

so both for my windows, as well as my linux installation, I am getting a Segmentation fault error message. On windows, only this gets printed, on Linux, I get Starting... Reading arguments... Done. Creating output and temporary directories... Done. Segmentation fault (core dumped)

Looking at the project code, I assume that for some reason, the program runs through a little further on Linux because of this. I tried both the nightly and stable build of c2d.

@sarthakpati mentioned that you might have insights here, @ludovenet ?

Edit: this also happens if I specify a temporary directory manually.

Best wishes Philippe

ludovenet commented 4 years ago

Hi Philippe,

Thank you for your interest in HistoReg.

It seems your error is due to an ITK function. What version of ITK do you use ? Are you sure it is compiled without errors ? Did you use it for other program ?

phiwei commented 4 years ago

Hi,

thanks for getting back to me. The ITK version is the one that gets compiled during the installation process in the guidelines. If I am not mistaken, that should be version 4.13.2, at least that is what I conclude from the folder names in the ITK directory within HistoReg - if this is not plausible, I can check again.

I do not use ITK for other purposes. During the process lined out in the guidelines, there are some warnings but no critical failures - it is still possible though that the process does not fully succeed.

  1. How can I check whether ITK compiled correctly?
  2. Can I download ITK from somewhere instead of building it myself? If so, to what folder would I need to paste it?

Best wishes Philippe

ludovenet commented 4 years ago

It should work perfectly if you installed ITK with our installer, so there is no point of compiling ITK individually. I am currently out of town with limited access to my computer. My holidays end this week end, I should be able to have more time to look into this next week, I will let you know when I have something new.

Best regards, Ludovic.

sarthakpati commented 4 years ago
  1. How can I check whether ITK compiled correctly?

If HistoReg got compiled, then it means that it was able to detect and link against ITK properly, which means that ITK was built properly.

EDIT: accidentally closed the issue.

sarthakpati commented 4 years ago

Hi Philippe,

Have you had a chance to try HistoReg's new release(s)? They make the process much easier to run and you don't need any further run-time installations.

Cheers!

phiwei commented 4 years ago

Hi,

thanks for pointing this out, I will see how it works in a month or two when I have some time!

Best wishes Philippe

sarthakpati commented 4 years ago

Alright! I am closing this issue, for now. If you run into further problems, please re-open or open a new one. 😄

erexhepa commented 3 years ago

Hi,

I was wondering if you could help with this issue as I do have the same problem. Just to answer the questions above, I am compiling ITK using the make shared in the git repository and everything goes smoothly. By the way I am getting the issue with the example images shared in the Data directory.

Thanks Elton

erexhepa commented 3 years ago

I manage to find a solution to the first "Segmentation fault" error. It appear $HistoReg variable it is not initialized properly during installation. If you use full paths it manages to start but there is still a "Segmentation fault" due to c2d executable. It is not found. Can you advise on how to install it ?

Best Elton

sarthakpati commented 3 years ago

Hi Elton,

Thanks for your interest in HistoReg!

Have you followed the superbuild recipe as mentioned in https://github.com/CBICA/HistoReg#windows or https://github.com/CBICA/HistoReg#linux?

The first make should compile ITK and the second should compile HistoReg and c2d...

erexhepa commented 3 years ago

Thank you very much for your quick feedback. Yeah I just realized I did a mistake on the second make (which would explain why HistoReg env variable was not setup properly). I am re-installing it again. Will give an update when I am finished.

sarthakpati commented 3 years ago

Awesome!

erexhepa commented 3 years ago

For the second cmake can I give as a prefix the same directory cloned from github ? If I want to install it in the same directory as ITK and all the other things that were build during the first cmake.

erexhepa commented 3 years ago

Thank you again for your assistance. By choosing the git repo to build the second make. It is working. Thank you for your work. Very useful.

sarthakpati commented 3 years ago

Glad to hear that it worked! If you publish your research please consider citing our paper.