# \#error **URL:** https://community.mrtrix.org/tag/error/8.md [Latest](https://community.mrtrix.org/latest.md) · [Categories](https://community.mrtrix.org/categories.md) · [Tags](https://community.mrtrix.org/tags.md) --- ## [Dwi2response Dhollander: extreme SDM tails causing very small CSF candidate pools](https://community.mrtrix.org/t/dwi2response-dhollander-extreme-sdm-tails-causing-very-small-csf-candidate-pools/8812)
**Author:** [@WilliamFCB](https://community.mrtrix.org/u/WilliamFCB)\ **Replies:** 0\ **Last updated:** [August 11, 2026, 5:17pm UTC](https://community.mrtrix.org/t/dwi2response-dhollander-extreme-sdm-tails-causing-very-small-csf-candidate-pools/8812 "2026-08-11T17:17:24Z")
Hi MRtrix3 team, @ThijsDhollander @jdtournier I am investigating reproducible dwi2response dhollander failures in a small number of subjects. After inspecting the retained temporary files, I now seem to have two related… --- ## [Configuration Error - Eigen - C++14](https://community.mrtrix.org/t/configuration-error-eigen-c-14/8638)
**Author:** [@lmoreau](https://community.mrtrix.org/u/lmoreau)\ **Replies:** 1\ **Last updated:** [February 2, 2026, 9:43am UTC](https://community.mrtrix.org/t/configuration-error-eigen-c-14/8638 "2026-02-02T09:43:42Z")
Hello, I am trying to install mrtrix3 on windows using the following instructions : Building MRtrix3 from source — MRtrix3 3.0 documentation However, I am encountering some issues when running “./configure”, I have the… --- ## [Tckconvert on whole-brain tractogram](https://community.mrtrix.org/t/tckconvert-on-whole-brain-tractogram/8596)
**Author:** [@pan4004](https://community.mrtrix.org/u/pan4004)\ **Replies:** 1\ **Last updated:** [November 18, 2025, 3:09am UTC](https://community.mrtrix.org/t/tckconvert-on-whole-brain-tractogram/8596 "2025-11-18T03:09:47Z")
Hi all, I have a whole-brain tractogram with 5 million streamlines and I an trying to extract the endpoint coordinates of each streamline with tckconvert: txt\_out = fullfile(outDir\_tmp , sprintf(‘%s\_%s\_endpoints-.txt’,… --- ## [Random Qt5 plugins linking issue](https://community.mrtrix.org/t/random-qt5-plugins-linking-issue/5875)
**Author:** [@j-tseng](https://community.mrtrix.org/u/j-tseng)\ **Replies:** 2\ **Last updated:** [November 18, 2025, 3:03am UTC](https://community.mrtrix.org/t/random-qt5-plugins-linking-issue/5875 "2025-11-18T03:03:27Z")
I had an issue and I solved it, and I figured I’d document it here in case anyone else runs into it. For some reason, after installing mrtrix3 through miniconda on Ubuntu 18.04, mrview didn’t work. It gave a linking erro… --- ## [Runing dwifslpreproc in MRtrix version 3.0.8, an error occurs: mean\_of\_first\_b0: Zero mean](https://community.mrtrix.org/t/runing-dwifslpreproc-in-mrtrix-version-3-0-8-an-error-occurs-mean-of-first-b0-zero-mean/8579)
**Author:** [@hao\_xu](https://community.mrtrix.org/u/hao_xu)\ **Replies:** 2\ **Last updated:** [November 18, 2025, 1:48am UTC](https://community.mrtrix.org/t/runing-dwifslpreproc-in-mrtrix-version-3-0-8-an-error-occurs-mean-of-first-b0-zero-mean/8579 "2025-11-18T01:48:46Z")
Hi everyone, I am currently using the latest version of MRtrix (3.0.8) with FSL software version 6.0.7.18 to process my single-phase encoding direction (AP, j-) data, which only has two b-values (b=0 and b=1000). I am c… --- ## [Dwifslpreproc fails with "unknown option -import\_pe\_table" (MRtrix3 3.0.7)](https://community.mrtrix.org/t/dwifslpreproc-fails-with-unknown-option-import-pe-table-mrtrix3-3-0-7/8515)
**Author:** [@raz27289](https://community.mrtrix.org/u/raz27289)\ **Replies:** 3\ **Last updated:** [October 14, 2025, 4:06pm UTC](https://community.mrtrix.org/t/dwifslpreproc-fails-with-unknown-option-import-pe-table-mrtrix3-3-0-7/8515 "2025-10-14T16:06:35Z")
Hello, I am running into an error with dwifslpreproc when preprocessing DWI data on macOS. System: macOS MRtrix version: 3.0.7 (mrconvert -version confirms) FSL: installed and available in $PATH Python: the wrapper sc… --- ## [Problem using MRtrix3Tissue alongside MRtrix3](https://community.mrtrix.org/t/problem-using-mrtrix3tissue-alongside-mrtrix3/8118)
**Author:** [@Tomm-C](https://community.mrtrix.org/u/Tomm-C)\ **Replies:** 2\ **Last updated:** [August 6, 2025, 1:59pm UTC](https://community.mrtrix.org/t/problem-using-mrtrix3tissue-alongside-mrtrix3/8118 "2025-08-06T13:59:58Z")
Hello, I’d like to use some functionalities of MRtrix3Tissue (ss3t\_csd\_beta1, specifically) while keeping MRtrix3 as the default source of commands. I have installed MRtrix3 in /usr/local/mrtrix3 and everything works f… --- ## [Issue : dwibiascorrect ants crashing terminal (moved from General Discussion to Development)](https://community.mrtrix.org/t/issue-dwibiascorrect-ants-crashing-terminal-moved-from-general-discussion-to-development/8383)
**Author:** [@A.Rossez](https://community.mrtrix.org/u/A.Rossez)\ **Replies:** 0\ **Last updated:** [June 3, 2025, 10:47am UTC](https://community.mrtrix.org/t/issue-dwibiascorrect-ants-crashing-terminal-moved-from-general-discussion-to-development/8383 "2025-06-03T10:47:44Z")
Hi Everyone ! :wave: :grinning: I already managed to tweak my code to bypass this issue (by coding an in-house use of N4BiasFieldCorrection) that I posted a while ago in General Discussion but since it looks like a majo… --- ## [Fixelcorrespondence error](https://community.mrtrix.org/t/fixelcorrespondence-error/8305)
**Author:** [@storrisi](https://community.mrtrix.org/u/storrisi)\ **Replies:** 2\ **Last updated:** [April 6, 2025, 3:48am UTC](https://community.mrtrix.org/t/fixelcorrespondence-error/8305 "2025-04-06T03:48:10Z")
hello experts! I’m at step 16 of the multi-tissue fixel pipeline (“Assign subject fixels to template fixels”) and up until now everything has been pretty smooth. For \>120 datasets I’m parallel-processing the pipeline on… --- ## [Issue : dwibiascorrect ants crashing terminal](https://community.mrtrix.org/t/issue-dwibiascorrect-ants-crashing-terminal/8301)
**Author:** [@A.Rossez](https://community.mrtrix.org/u/A.Rossez)\ **Replies:** 0\ **Last updated:** [March 25, 2025, 4:05pm UTC](https://community.mrtrix.org/t/issue-dwibiascorrect-ants-crashing-terminal/8301 "2025-03-25T16:05:11Z")
Hi Everyone ! :wave: :grinning: I am once again asking for help on some issue: :sweat\_smile: I am trying to use dwibiascorrect ants on my diffusion data (Rodent data, 15 directions, single-shell) before generating FODs… --- ## [The solution to \[error\] Library not loaded when running mrinfo/dcminfo](https://community.mrtrix.org/t/the-solution-to-error-library-not-loaded-when-running-mrinfo-dcminfo/8282)
**Author:** [@StarVolcano](https://community.mrtrix.org/u/StarVolcano)\ **Replies:** 0\ **Last updated:** [March 14, 2025, 5:55am UTC](https://community.mrtrix.org/t/the-solution-to-error-library-not-loaded-when-running-mrinfo-dcminfo/8282 "2025-03-14T05:55:28Z")
When running mrinfo/dcminfo on my Mac (Sequoia 15.3), I encountered an error: dyld\[63980\]: Library not loaded: /opt/homebrew/opt/libtiff/lib/libtiff.5.dylib Referenced from: \<08BFBB0E-2142-310B-A3F5-3D3789076AC9\> /Use… --- ## [Problems when using sh2peaks](https://community.mrtrix.org/t/problems-when-using-sh2peaks/3950)
**Author:** [@luyuhengCN](https://community.mrtrix.org/u/luyuhengCN)\ **Replies:** 5\ **Last updated:** [March 3, 2025, 4:27pm UTC](https://community.mrtrix.org/t/problems-when-using-sh2peaks/3950 "2025-03-03T16:27:12Z")
Hi, I came across an problem when using sh2peak to get the orientation vector. Here is the command: sh2peaks wmfod.mif -num 1 peaks\_first.nii.gz Then, I checked the nii image with fsleyes, finding the orientation is i… --- ## [Tckedit ](https://community.mrtrix.org/t/tckedit/8253)
**Author:** [@samia](https://community.mrtrix.org/u/samia)\ **Replies:** 0\ **Last updated:** [February 27, 2025, 6:28pm UTC](https://community.mrtrix.org/t/tckedit/8253 "2025-02-27T18:28:43Z")
Hello, I’m getting an error on trying to run tckedit: \[ERROR\] Unable to parse text “path to file/sub-23362\_RR-ses-D1\_normalized.mif” as a ROI tckedit: \[ERROR\] If interpreted as sphere: tckedit: \[ERROR\] error conve… --- ## [MRview crashes when viewing connectome as Geometry: Overlay and turning on Crop to Slab](https://community.mrtrix.org/t/mrview-crashes-when-viewing-connectome-as-geometry-overlay-and-turning-on-crop-to-slab/8075)
**Author:** [@samuelholly](https://community.mrtrix.org/u/samuelholly)\ **Replies:** 0\ **Last updated:** [November 26, 2024, 12:20pm UTC](https://community.mrtrix.org/t/mrview-crashes-when-viewing-connectome-as-geometry-overlay-and-turning-on-crop-to-slab/8075 "2024-11-26T12:20:15Z")
Dear all, I would like to ask for help. I tried to view my parcellation with Geometry set to Overlay in the Connectome tool in MRview. When I tried to activate the Crop to Slab option, MRview crashed and the terminal s… --- ## [MRtrix3Tissue ss3t\_csd\_beta1 not running](https://community.mrtrix.org/t/mrtrix3tissue-ss3t-csd-beta1-not-running/8042)
**Author:** [@Tomm-C](https://community.mrtrix.org/u/Tomm-C)\ **Replies:** 1\ **Last updated:** [November 3, 2024, 11:15am UTC](https://community.mrtrix.org/t/mrtrix3tissue-ss3t-csd-beta1-not-running/8042 "2024-11-03T11:15:55Z")
Hi all, I have installed MRtrix3Tissue and set the path to it in my my .zsh startup file. The path to the MRtrix3Tissue directory is /Users/myusername/MRtrix3Tissue. The path to the python3 directory is /usr/local/bin/… --- ## [TractSeg ImportError: cannot import name 'trackvis' from 'nibabel'](https://community.mrtrix.org/t/tractseg-importerror-cannot-import-name-trackvis-from-nibabel/7975)
**Author:** [@Hasini\_Weerathunge](https://community.mrtrix.org/u/Hasini_Weerathunge)\ **Replies:** 1\ **Last updated:** [October 9, 2024, 3:02am UTC](https://community.mrtrix.org/t/tractseg-importerror-cannot-import-name-trackvis-from-nibabel/7975 "2024-10-09T03:02:51Z")
This is not strictly MRtrix installation related but I am having a hard time trying to get TractSeg running with MRtrix. I get the following error - any help would be greatly appreciated! ImportError: cannot import nam… --- ## [5ttgen hsvs lesion](https://community.mrtrix.org/t/5ttgen-hsvs-lesion/6295)
**Author:** [@Lucius](https://community.mrtrix.org/u/Lucius)\ **Replies:** 5\ **Last updated:** [September 3, 2024, 12:06am UTC](https://community.mrtrix.org/t/5ttgen-hsvs-lesion/6295 "2024-09-03T00:06:03Z")
Hi, While using 5ttgen hsvs, we noticed that the brainstem is assigned to volume 4 (pathological tissue) with the hsvs algorithm, cf screenshot 1. Although the 5ttgen hsvs algorithm includes the option to assign the br… --- ## [Labelconvert](https://community.mrtrix.org/t/labelconvert/7642)
**Author:** [@Owl](https://community.mrtrix.org/u/Owl)\ **Replies:** 1\ **Last updated:** [June 19, 2024, 2:55am UTC](https://community.mrtrix.org/t/labelconvert/7642 "2024-06-19T02:55:49Z")
Hi all When I was using labelconvert to convert label files, the following error message appeared. Does anyone know how to solve it? labelconvert: \[ERROR\] LUT file “BN\_Atlas\_246\_LUT\_new.txt” in unrecognized format: la… --- ## [Eddy\_cuda error](https://community.mrtrix.org/t/eddy-cuda-error/7729)
**Author:** [@Qianhui\_Xu](https://community.mrtrix.org/u/Qianhui_Xu)\ **Replies:** 0\ **Last updated:** [June 15, 2024, 11:15am UTC](https://community.mrtrix.org/t/eddy-cuda-error/7729 "2024-06-15T11:15:20Z")
Hello experts! I recently attempted to use eddy\_cuda for preprocessing DWI data. However, after running dwifslpreproc, I encountered an error indicating ‘CUDA version is not successful.’ Subsequently, eddy\_opmemp starte… --- ## [Batch Processing error](https://community.mrtrix.org/t/batch-processing-error/7644)
**Author:** [@Sebastian\_Navarrete](https://community.mrtrix.org/u/Sebastian_Navarrete)\ **Replies:** 0\ **Last updated:** [May 17, 2024, 9:07pm UTC](https://community.mrtrix.org/t/batch-processing-error/7644 "2024-05-17T21:07:43Z")
Hello everyone, I am applying mrthreshold to obtain a binary image from a density image. I want to perform this processing for each of the subfolders I have. The folders are organized as follows: TractSeg\_64\_atlas/A… --- ## [Tckgen: \[SYSTEM FATAL CODE: SIGSEGV (11)\] Segmentation fault: Invalid memory access (DYNAMIC SEEDING)](https://community.mrtrix.org/t/tckgen-system-fatal-code-sigsegv-11-segmentation-fault-invalid-memory-access-dynamic-seeding/7593)
**Author:** [@Hank\_Golding](https://community.mrtrix.org/u/Hank_Golding)\ **Replies:** 2\ **Last updated:** [May 16, 2024, 7:19pm UTC](https://community.mrtrix.org/t/tckgen-system-fatal-code-sigsegv-11-segmentation-fault-invalid-memory-access-dynamic-seeding/7593 "2024-05-16T19:19:41Z")
Hello all, I am running MRTrix3 3.0.4, producing connectomes with dynamic seeding using tckgen with the IFOD2 option. I have run this command on 10 brains - 9 work perfectly, one repeatedly fails: tckgen: \[DEBUG\] No co… --- ## [Mrview version 3.0.4 crashed](https://community.mrtrix.org/t/mrview-version-3-0-4-crashed/7327)
**Author:** [@hyting](https://community.mrtrix.org/u/hyting)\ **Replies:** 2\ **Last updated:** [February 5, 2024, 8:32am UTC](https://community.mrtrix.org/t/mrview-version-3-0-4-crashed/7327 "2024-02-05T08:32:38Z")
Dear MRtrix experts, Yesterday, when I tried to run mrview, it crashed. And I have viewed this issue in some old threads, it seems this can generally solved by updating. However, my mrview version is 3.0.4, already the … --- ## [Install Mrtrix3 via conda successufly but fail to open in Ubuntu 22.04.3](https://community.mrtrix.org/t/install-mrtrix3-via-conda-successufly-but-fail-to-open-in-ubuntu-22-04-3/7236)
**Author:** [@Roger1219](https://community.mrtrix.org/u/Roger1219)\ **Replies:** 3\ **Last updated:** [December 19, 2023, 10:24am UTC](https://community.mrtrix.org/t/install-mrtrix3-via-conda-successufly-but-fail-to-open-in-ubuntu-22-04-3/7236 "2023-12-19T10:24:29Z")
Hi experts, I have used mrtrix3 for a while. Recently, I tried to install Mrtrix3 in a new PC with Ubuntu 22.04.3. I created a new conda environment with python 3.11 and execute the following code without any errors: c… --- ## [Issue with Negative Intensity Values in Left ROI After Transformation Using ANTs and MRtrix](https://community.mrtrix.org/t/issue-with-negative-intensity-values-in-left-roi-after-transformation-using-ants-and-mrtrix/7128)
**Author:** [@Shai\_P](https://community.mrtrix.org/u/Shai_P)\ **Replies:** 2\ **Last updated:** [December 15, 2023, 11:01am UTC](https://community.mrtrix.org/t/issue-with-negative-intensity-values-in-left-roi-after-transformation-using-ants-and-mrtrix/7128 "2023-12-15T11:01:04Z")
Hi everyone, I’m working on warping ROIs from MNI space to a subject’s native FA space using ANTs and MRtrix. After applying transformations, I noticed that while the right ROI looks normal (intensity values ranging fro… --- ## [Fod2fixel not working](https://community.mrtrix.org/t/fod2fixel-not-working/6211)
**Author:** [@polivaoren](https://community.mrtrix.org/u/polivaoren)\ **Replies:** 1\ **Last updated:** [December 8, 2023, 9:18am UTC](https://community.mrtrix.org/t/fod2fixel-not-working/6211 "2023-12-08T09:18:22Z")
Hi. I’m following the ‘Fibre density and cross section -Multi tissue CSD’ tutorial. I’ve finished running through the entire pipeline just to discover that almost all the files are mostly empty (they do have 1-10 random … --- ## [dStripe module for MRtrix](https://community.mrtrix.org/t/dstripe-module-for-mrtrix/7131)
**Author:** [@Bradley\_Wilkes](https://community.mrtrix.org/u/Bradley_Wilkes)\ **Replies:** 0\ **Last updated:** [November 17, 2023, 8:24pm UTC](https://community.mrtrix.org/t/dstripe-module-for-mrtrix/7131 "2023-11-17T20:24:55Z")
Hello MRtrix community, I am attempting to use the dStripe module for MRtrix developed by @maxpietsch ( GitHub - maxpietsch/dStripe: This repository contains code and model weights for the method described in the paper… --- ## [Bug with MRview on MacOS Sonoma](https://community.mrtrix.org/t/bug-with-mrview-on-macos-sonoma/7109)
**Author:** [@michefabb](https://community.mrtrix.org/u/michefabb)\ **Replies:** 2\ **Last updated:** [November 12, 2023, 9:38pm UTC](https://community.mrtrix.org/t/bug-with-mrview-on-macos-sonoma/7109 "2023-11-12T21:38:23Z")
Dear MRtrix experts, I updated my machine from MacOS Ventura with Intel silicon to a more recent MacOS Sonoma 14.1.1 with Apple Silicon. Following this, when opening MRview I get the following error in the Terminal: “… --- ## [Dwifslpreproc Fails with EDDY::: Eddy failed with message Error](https://community.mrtrix.org/t/dwifslpreproc-fails-with-eddy-eddy-failed-with-message-error/6930)
**Author:** [@Shai\_P](https://community.mrtrix.org/u/Shai_P)\ **Replies:** 3\ **Last updated:** [September 22, 2023, 1:26am UTC](https://community.mrtrix.org/t/dwifslpreproc-fails-with-eddy-eddy-failed-with-message-error/6930 "2023-09-22T01:26:42Z")
Hello everyone, I am experiencing an issue while running the dwifslpreproc script on my dataset. The process appears to be running fine until it reaches the eddy\_cpu command, after which it fails with a vague error mess… --- ## [Nodes without streamlines assigned AAL3 atlas](https://community.mrtrix.org/t/nodes-without-streamlines-assigned-aal3-atlas/6927)
**Author:** [@mariacaranova](https://community.mrtrix.org/u/mariacaranova)\ **Replies:** 3\ **Last updated:** [September 5, 2023, 8:08am UTC](https://community.mrtrix.org/t/nodes-without-streamlines-assigned-aal3-atlas/6927 "2023-09-05T08:08:43Z")
Dear all, I am currently trying to compute a connectome using tractography data from MRtrix3 (10M streamlines) and AAL3 atlas parcellations. I registered the AAL3 atlas template into diffusion space, and everything seem… --- ## [ss3t\_csd\_beta1 Segmentation fault: Invalid memory access](https://community.mrtrix.org/t/ss3t-csd-beta1-segmentation-fault-invalid-memory-access/6922)
**Author:** [@dafhafhajfajfna](https://community.mrtrix.org/u/dafhafhajfajfna)\ **Replies:** 0\ **Last updated:** [September 3, 2023, 9:32am UTC](https://community.mrtrix.org/t/ss3t-csd-beta1-segmentation-fault-invalid-memory-access/6922 "2023-09-03T09:32:44Z")
HiMRtrixExperts, When I ran the command “ss3t\_csd\_beta1 ss3t\_csd\_fod\_path/data\_b1000\_g32.mif ss3t\_csd\_fod\_path/RF\_WM.txt ss3t\_csd\_fod\_path/WM\_FODs.nii.gz ss3t\_csd\_fod\_path/RF\_GM.txt ss3t\_csd\_fod\_path/GM\_FODs.nii.gz ss3t… [Next page](https://community.mrtrix.org/tag/error/8.md?match_all_tags=true&page=1&tags%5B%5D=error)