bug fixes for new v2.3.0 #80
Replies: 4 comments 22 replies
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Hi @neurotix93, Thanks for the kind words and useful feedback! What version are you using? This is always important to mention as the software been updating very rapidly. From your screenshot, it looks like it is a path issue. Version 2.3.0 should be good to go as I tested it both in GUI and scripting. |
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Hello, Thank you so much - it is working now. Subject atlas segmentation: Started Seems to be an error with the atlas? |
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Here is potentially another small bug with QSIPrep -- as I want to incorporate anisotropic conductivities into the modelling. Beginning pre-processing for subject: 002 Also, I cannot see if the TIToolbox call to QSIPrep allows the use of reverse phase encoded data stored in a directory like fmap for distortion correction? Is that possible? |
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Hi @neurotix93 — quick update: several preprocessing/QSI follow-ups related to this thread have now been addressed and are queued for v2.3.1. The release will include preprocessing cleanup, better GUI process/error reporting, and an upgrade of QSIPrep/QSIRecon to PennLINC These updates should be released with v2.3.1 in the coming days. If anything persists after updating, please share the new log output and I’ll follow up from there. p.s. Would love to hear if you ran any comparison with previous DTI pipelines and can share either qualitative or quantitative results. Best, |
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Hello
Thank you for the wonderful toolbox!
In the preprocessing step, the tissue analysis is failing with the following error:
2026-03-17 19:58:30 | INFO | pre.preprocess.002 | ├─ FreeSurfer recon-all: ✓ Complete
2026-03-17 19:58:30 | INFO | pre.preprocess.002 | ├─ Tissue analysis: Started
2026-03-17 19:58:30 | ERROR | pre.preprocess.002 | Tissue analysis failed: Labeling.nii.gz not found at /mnt/derivatives/SimNIBS/sub-002/m2m_002/segmentation/Labeling.nii.gz
2026-03-17 19:58:30 | INFO | pre.preprocess.002 | ├─ Tissue analysis: ✗ Failed
2026-03-17 19:58:30 | INFO | pre.preprocess.002 | └─ Pre-processing failed for subject: 002
I wonder if there is a bug, as SimNIBS produces a file called 'labeling.nii.gz' which seems to be the correct file, so maybe there is a case sensitivity issue?
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