# \#preprocessing **URL:** https://community.mrtrix.org/tag/preprocessing/10.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… --- ## [Question about FBA sensitivity to mask quality](https://community.mrtrix.org/t/question-about-fba-sensitivity-to-mask-quality/8695)
**Author:** [@aknodt](https://community.mrtrix.org/u/aknodt)\ **Replies:** 3\ **Last updated:** [April 22, 2026, 12:41pm UTC](https://community.mrtrix.org/t/question-about-fba-sensitivity-to-mask-quality/8695 "2026-04-22T12:41:09Z")
I am new to FBA but seem to have successfully executed the analysis for most of the subjects in my dataset. One of the things I am QC’ing on everyone is the quality of the mask, and I’ve found that quite a few seem to b… --- ## [Eddy not correcting movement](https://community.mrtrix.org/t/eddy-not-correcting-movement/8598)
**Author:** [@Petr\_C](https://community.mrtrix.org/u/Petr_C)\ **Replies:** 1\ **Last updated:** [November 18, 2025, 3:15am UTC](https://community.mrtrix.org/t/eddy-not-correcting-movement/8598 "2025-11-18T03:15:19Z")
Hi community, I know this may not be the ideal place to post this since it is more of an EDDY issue, but I was hoping that someone has encountered something similar and found a solution. I’m having problems with prepro… --- ## [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… --- ## [Zero-filled volumes after applytopup within dwifslpreproc](https://community.mrtrix.org/t/zero-filled-volumes-after-applytopup-within-dwifslpreproc/8612)
**Author:** [@hao\_xu](https://community.mrtrix.org/u/hao_xu)\ **Replies:** 1\ **Last updated:** [November 18, 2025, 1:37am UTC](https://community.mrtrix.org/t/zero-filled-volumes-after-applytopup-within-dwifslpreproc/8612 "2025-11-18T01:37:09Z")
Hello, I’m currently experiencing the same issue. After troubleshooting, I discovered that when executing the following command with dwifslpreproc, all output file values are set to zero. Command: applytopup --imain=ap… --- ## [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… --- ## [Registering mask in FLAIR space to FBA template space](https://community.mrtrix.org/t/registering-mask-in-flair-space-to-fba-template-space/8488)
**Author:** [@LM10](https://community.mrtrix.org/u/LM10)\ **Replies:** 0\ **Last updated:** [August 12, 2025, 8:01pm UTC](https://community.mrtrix.org/t/registering-mask-in-flair-space-to-fba-template-space/8488 "2025-08-12T20:01:41Z")
Hi everyone, I’d like to use a lesion mask that’s derived from FLAIR images in subject space on my FBA output to look at average FDC within the lesions and to also use CFE within the masked areas. I can’t seem to make t… --- ## [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… --- ## [\[labelconvert\] bilateral thalamus gone](https://community.mrtrix.org/t/labelconvert-bilateral-thalamus-gone/1580)
**Author:** [@Jiook\_Cha](https://community.mrtrix.org/u/Jiook_Cha)\ **Replies:** 6\ **Last updated:** [July 28, 2025, 10:01am UTC](https://community.mrtrix.org/t/labelconvert-bilateral-thalamus-gone/1580 "2025-07-28T10:01:06Z")
Hi Rob, In my group analysis (N=~200), I found that labelconvert “skipped” specifically the bilateral thalamus. No error messages until I ran tck2connectome: tck2connectome: \[WARNING\] existing output files will be ove… --- ## [CSF voxel selection in dwi2response dhollander skips ventricles, expected?](https://community.mrtrix.org/t/csf-voxel-selection-in-dwi2response-dhollander-skips-ventricles-expected/8432)
**Author:** [@AndreasP](https://community.mrtrix.org/u/AndreasP)\ **Replies:** 2\ **Last updated:** [July 2, 2025, 9:53am UTC](https://community.mrtrix.org/t/csf-voxel-selection-in-dwi2response-dhollander-skips-ventricles-expected/8432 "2025-07-02T09:53:14Z")
Greetings MRTrix community and experts! This will be my first post, first of many I would assume :sweat\_smile:. I want to start of by giving some background about my knowledge of the area: at the moment of writing this … --- ## [Order of preprocessing steps with already eddy corrected data](https://community.mrtrix.org/t/order-of-preprocessing-steps-with-already-eddy-corrected-data/7798)
**Author:** [@FabianKTH](https://community.mrtrix.org/u/FabianKTH)\ **Replies:** 1\ **Last updated:** [June 5, 2025, 4:20am UTC](https://community.mrtrix.org/t/order-of-preprocessing-steps-with-already-eddy-corrected-data/7798 "2025-06-05T04:20:59Z")
Hi, I find myself in a situation where my collaboration provides only preprocessed eddy-corrected dwi data (no denoising/deringing). I’m aware that based on this post andthis post the recommended preprocessing order see… --- ## [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… --- ## [Handling Negative Values After mrdegibbs and Tensor Estimation](https://community.mrtrix.org/t/handling-negative-values-after-mrdegibbs-and-tensor-estimation/8372)
**Author:** [@Javier](https://community.mrtrix.org/u/Javier)\ **Replies:** 1\ **Last updated:** [May 29, 2025, 8:37am UTC](https://community.mrtrix.org/t/handling-negative-values-after-mrdegibbs-and-tensor-estimation/8372 "2025-05-29T08:37:50Z")
Hello MRtrix3 community, I’ve been running my preprocessing pipeline without technical errors, but I’ve encountered an issue regarding negative values in my diffusion tensor and MD images, and I’d appreciate your insigh… --- ## [Dwi2mask generates full-white mask instead of brain](https://community.mrtrix.org/t/dwi2mask-generates-full-white-mask-instead-of-brain/8343)
**Author:** [@Javier](https://community.mrtrix.org/u/Javier)\ **Replies:** 2\ **Last updated:** [May 4, 2025, 3:27pm UTC](https://community.mrtrix.org/t/dwi2mask-generates-full-white-mask-instead-of-brain/8343 "2025-05-04T15:27:12Z")
Hello, The code below is part of my preprocessing pipeline, which I ran in Neurodesk using MRtrix3 (version 3.0.4). My DWI data is multi-shell, with 1 b=0, 64 b=1500, and 64 b=3000 volumes (PhaseEncodingDirection = j). … --- ## [Warping of DWI in Spherical Harmonic Coefficient form](https://community.mrtrix.org/t/warping-of-dwi-in-spherical-harmonic-coefficient-form/8314)
**Author:** [@FabianKTH](https://community.mrtrix.org/u/FabianKTH)\ **Replies:** 0\ **Last updated:** [April 4, 2025, 8:24am UTC](https://community.mrtrix.org/t/warping-of-dwi-in-spherical-harmonic-coefficient-form/8314 "2025-04-04T08:24:50Z")
Hi everybody! I have a Situation where I want to apply a nonlinear deformation (a warp) from a registration to a Diffusion weighted Image (DWI). In order not to depend on gradient directions (and for further processing)… --- ## [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… --- ## [Mtnormalise results on HCP data](https://community.mrtrix.org/t/mtnormalise-results-on-hcp-data/8299)
**Author:** [@Roey\_Schurr](https://community.mrtrix.org/u/Roey_Schurr)\ **Replies:** 0\ **Last updated:** [March 25, 2025, 1:35pm UTC](https://community.mrtrix.org/t/mtnormalise-results-on-hcp-data/8299 "2025-03-25T13:35:44Z")
Dear MRtrix’ers, I’m working on HCP data, closely following the Nature Protocol paper: Calculate tissue-specific response functions using dwi2response dhollander. Average response functions across subjects using respo… --- ## [Integrating Synb0-DISCO with dwifslpreproc](https://community.mrtrix.org/t/integrating-synb0-disco-with-dwifslpreproc/7571)
**Author:** [@Bastiaan\_van\_Tol](https://community.mrtrix.org/u/Bastiaan_van_Tol)\ **Replies:** 3\ **Last updated:** [March 16, 2025, 7:47pm UTC](https://community.mrtrix.org/t/integrating-synb0-disco-with-dwifslpreproc/7571 "2025-03-16T19:47:26Z")
Hi everyone, I have two main questions about inhomogeneity distortion correction in MRtrix; one about how to best integrate Synb0-DISCO’s output within dwifslpreproc, and one about a specific error I get when running to… --- ## [ROI tractography](https://community.mrtrix.org/t/roi-tractography/8207)
**Author:** [@samia](https://community.mrtrix.org/u/samia)\ **Replies:** 0\ **Last updated:** [February 7, 2025, 6:24pm UTC](https://community.mrtrix.org/t/roi-tractography/8207 "2025-02-07T18:24:28Z")
Hello MRtrix3 experts, I have been trying to compare the effects of optic nerve crush on the left eye versus the right eye of the same subject as the control. A cluster shows up there on one side of the brain in the hip… --- ## [Tractogram Validation](https://community.mrtrix.org/t/tractogram-validation/8120)
**Author:** [@raena](https://community.mrtrix.org/u/raena)\ **Replies:** 1\ **Last updated:** [February 2, 2025, 1:59pm UTC](https://community.mrtrix.org/t/tractogram-validation/8120 "2025-02-02T13:59:37Z")
Dear MRtrix3 Team, Hello, I hope this post finds you well. I generated a probabilistic (iFOD2) tractogram, as shown in the image below: While it appears valid, many responses I’ve seen in the community suggest that a … --- ## [Dwidenoise "excluded voxels"](https://community.mrtrix.org/t/dwidenoise-excluded-voxels/8154)
**Author:** [@aroliveira](https://community.mrtrix.org/u/aroliveira)\ **Replies:** 0\ **Last updated:** [January 15, 2025, 12:21pm UTC](https://community.mrtrix.org/t/dwidenoise-excluded-voxels/8154 "2025-01-15T12:21:19Z")
Dear community, I am currently using dwidenoise to process a set of diffusion images with 585 volumes acquired at different diffusion times for a rat brain. However, I have encountered an issue I hope you can help clari… --- ## [Strange artifact in DWI - differential slice-wise scaling in AP directions](https://community.mrtrix.org/t/strange-artifact-in-dwi-differential-slice-wise-scaling-in-ap-directions/1219)
**Author:** [@Antonin\_Skoch](https://community.mrtrix.org/u/Antonin_Skoch)\ **Replies:** 4\ **Last updated:** [October 14, 2024, 10:46am UTC](https://community.mrtrix.org/t/strange-artifact-in-dwi-differential-slice-wise-scaling-in-ap-directions/1219 "2024-10-14T10:46:10Z")
Dear experts, I am writing this post in the hope that you can help me to correct for following artifact I encounter in the data of one of our studies. This artifact is manifesting by differential slice-wise scaling in A… --- ## [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… --- ## [Issue with dwifslpreproc](https://community.mrtrix.org/t/issue-with-dwifslpreproc/7870)
**Author:** [@polivaoren](https://community.mrtrix.org/u/polivaoren)\ **Replies:** 0\ **Last updated:** [August 16, 2024, 8:34pm UTC](https://community.mrtrix.org/t/issue-with-dwifslpreproc/7870 "2024-08-16T20:34:26Z")
Hello. I’m trying to conduct tractography on a monkey DTI data set from Aix-Marseille Université I found online (https://fcon\_1000.projects.nitrc.org/indi/PRIMEdownloads.html). I tried to run several versions of dwifslp… --- ## [HCP dwi data pre](https://community.mrtrix.org/t/hcp-dwi-data-pre/7837)
**Author:** [@Owl](https://community.mrtrix.org/u/Owl)\ **Replies:** 2\ **Last updated:** [July 28, 2024, 10:36am UTC](https://community.mrtrix.org/t/hcp-dwi-data-pre/7837 "2024-07-28T10:36:45Z")
Hi all, I’m working on HCP dwi data, according to GitHub - civier/HCP-dMRI-connectome: MRtrix scripts to generate dense weighted structural connectomes from the Human Connectome Project "minimally pre-processed" diffusi… --- ## [Question on Tensor Fitting with Single vs. Multishell Data in MRtrix3](https://community.mrtrix.org/t/question-on-tensor-fitting-with-single-vs-multishell-data-in-mrtrix3/7347)
**Author:** [@CarlisleYun79](https://community.mrtrix.org/u/CarlisleYun79)\ **Replies:** 6\ **Last updated:** [July 16, 2024, 6:21am UTC](https://community.mrtrix.org/t/question-on-tensor-fitting-with-single-vs-multishell-data-in-mrtrix3/7347 "2024-07-16T06:21:13Z")
Dear MRtrix3 experts, I have a question regarding the tensor fitting process for analyzing diffusion maps, specifically about how it differs between single shell and multishell data. According to the mrtrix3 manual, I … --- ## [Multi shell tensor fitting](https://community.mrtrix.org/t/multi-shell-tensor-fitting/7788)
**Author:** [@JON4321](https://community.mrtrix.org/u/JON4321)\ **Replies:** 1\ **Last updated:** [July 9, 2024, 9:41am UTC](https://community.mrtrix.org/t/multi-shell-tensor-fitting/7788 "2024-07-09T09:41:20Z")
Hi all, I have multi-shell diffusion data, b=0, b=1000, b=2000. When processing the data using MRtrix tools I would like to do tensor fitting as well. Does dwi2tensor use all b-values, or just b=1000 as this is where g… --- ## [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… --- ## [DWI preprocessing dwi2response output differences between subjects](https://community.mrtrix.org/t/dwi-preprocessing-dwi2response-output-differences-between-subjects/7691)
**Author:** [@nicolas.tempier](https://community.mrtrix.org/u/nicolas.tempier)\ **Replies:** 1\ **Last updated:** [May 31, 2024, 10:59am UTC](https://community.mrtrix.org/t/dwi-preprocessing-dwi2response-output-differences-between-subjects/7691 "2024-05-31T10:59:14Z")
Dear Mrtrix community, I am contacting you about the differences that I observe on the response functions of two different exvivo specimens in the same structures (Globus pallidus) in human. The sequences were the same… --- ## [Fail to make eddy\_options work when calling dwifslpreproc from Windows via WSL](https://community.mrtrix.org/t/fail-to-make-eddy-options-work-when-calling-dwifslpreproc-from-windows-via-wsl/7676)
**Author:** [@zzwang](https://community.mrtrix.org/u/zzwang)\ **Replies:** 1\ **Last updated:** [May 30, 2024, 8:04am UTC](https://community.mrtrix.org/t/fail-to-make-eddy-options-work-when-calling-dwifslpreproc-from-windows-via-wsl/7676 "2024-05-30T08:04:16Z")
Hi all, I installed MRtrix in WSL on my Windows laptop. I managed to run the MRtrix functions in MATLAB (installed in the Windows system, not WSL) via the ‘system’ function, and it works pretty well in many cases. Howeve… [Next page](https://community.mrtrix.org/tag/preprocessing/10.md?match_all_tags=true&page=1&tags%5B%5D=preprocessing)