Hi, I have trouble using FreeSurfer Importer provided with the SlicerFreSurfer extension. Problem: When I try to load segmentation, it cuases bad_alloc error. The error message is below. “Slicer has caught an application error, please save your work and restart.\n\nThe application has run out of …

Thanks for reporting this. QXcbConnection: XCB error: 3 (BadWindow)... message is just a warning (seems to be a known Qt bug ). Probably it is not the root cause of the serious std::bad_alloc error, but the QXcbConnection error may be triggered by the display of the modal error popup. The memory al…

Thank you for the prompt reply. I have this problem with even “bert” data shipped with FreeSurfer 7.3.2. (None of aseg.mgz(s) cannot be loaded) This is what I did. Copy bert to my home directory mkdir -p ~/freesurfer/7.3.2/subjects cp -r $FRESURFER_HOME/subjects/bert ~/freesurfer/7.3.2/subjec…

I have not been able to reproduce this issue using the steps above in the following setup: OS: Ubuntu 22.04 Slicer version: 5.3.0-2022-12-03 (self-built) Slicer revision: 31346 SlicerFreeSurfer: master branch @kytk , you could give a try to the preview release (5.3.0) and see if it works. From a…

Thank you for checking. Now I know that something is wrong in my environment. Though the preview release resulted in the same error, I will try to build Slicer for my environment and see if it works.

Chiming in late, but I am also getting this issue with 5.3.0 and Ubuntu 22.04. I did not have this issue on Windows or Mac with the same dataset and Slicer Version. It seems to throw the error specifically when loading Segmentations from FreeSurfer, I’m able to load Models and Volumes. I have ple…

Try the latest release and preview release (5.3.0 is old at this point). Also, if the issue can be easily reproduced, please share data and exact steps that lead to the issue.

bad_alloc error in slicerfreesurfer on 5.2.1 Linux

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Topic		Replies	Views
Error loading freesurfer segmentation Support freesurfer	6	795	November 11, 2023
SlicerFreeSurfer runs out of memory to load wmparc.mgz Support freesurfer	1	66	April 17, 2025
Internal error : Bad array new length Support segmentation	3	1053	February 13, 2020
Bad allocation exception Support	5	2464	June 24, 2020
Bad_alloc error while using margin effect in Segment editor module Support	1	511	June 10, 2020

bad_alloc error in slicerfreesurfer on 5.2.1 Linux

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