# Latest **URL:** https://community.mrtrix.org/latest.md?page=2 [Latest](https://community.mrtrix.org/latest.md) · [Categories](https://community.mrtrix.org/categories.md) · [Tags](https://community.mrtrix.org/tags.md) **Page:** 3 --- ## [Inquiry regarding the extraction of Diffusion Tensor metrics](https://community.mrtrix.org/t/inquiry-regarding-the-extraction-of-diffusion-tensor-metrics/8731)
**Author:** [@Dr.quocvan](https://community.mrtrix.org/u/Dr.quocvan)\ **Replies:** 0\ **Last updated:** [April 1, 2026, 8:05am UTC](https://community.mrtrix.org/t/inquiry-regarding-the-extraction-of-diffusion-tensor-metrics/8731 "2026-04-01T08:05:09Z")
Dear Expert, I have a technical question regarding the processing of DTI data for anatomical consistency. Assuming I have already obtained the unique 3x3 Diffusion Tensor matrix (D) solved via Least Squares from 64-dir… --- ## [Ways to quantitatively compare endpoint "densities"](https://community.mrtrix.org/t/ways-to-quantitatively-compare-endpoint-densities/8722)
**Author:** [@Ranesh](https://community.mrtrix.org/u/Ranesh)\ **Replies:** 5\ **Last updated:** [March 31, 2026, 12:43pm UTC](https://community.mrtrix.org/t/ways-to-quantitatively-compare-endpoint-densities/8722 "2026-03-31T12:43:32Z")
Hi all, I was wondering if anyone has suggestions on how to obtain a numerical measure of endpoint distribution that could be used in downstream statistical analyses. For context, we are performing ROI–ROI tractography … --- ## [“--slm=linear”: is an unrecognised token!](https://community.mrtrix.org/t/slm-linear-is-an-unrecognised-token/8730)
**Author:** [@Jianjian](https://community.mrtrix.org/u/Jianjian)\ **Replies:** 1\ **Last updated:** [March 31, 2026, 11:46am UTC](https://community.mrtrix.org/t/slm-linear-is-an-unrecognised-token/8730 "2026-03-31T11:46:04Z")
Dear all, I am following BATMAN structure to run test codes (MRtrix3.0.8 on a macbook M4): Now I want to run motion and distortion correction with dwifslpreproc command: dwifslpreproc dwi\_den\_unr.mif dwi\_den\_unr\_prepr… --- ## [How to use tckgen to generate fibers that start from ROI A, pass through ROIs B, C, and D, and terminate at ROI E?](https://community.mrtrix.org/t/how-to-use-tckgen-to-generate-fibers-that-start-from-roi-a-pass-through-rois-b-c-and-d-and-terminate-at-roi-e/8728)
**Author:** [@LiuYuchen](https://community.mrtrix.org/u/LiuYuchen)\ **Replies:** 2\ **Last updated:** [March 31, 2026, 5:30am UTC](https://community.mrtrix.org/t/how-to-use-tckgen-to-generate-fibers-that-start-from-roi-a-pass-through-rois-b-c-and-d-and-terminate-at-roi-e/8728 "2026-03-31T05:30:50Z")
Hi all, Could you please share your experiences on how to use tckgen to generate fibers that start from ROI A, pass through ROIs B, C, and D, and terminate at ROI E? --- ## [Extracting fixels along the X, Y, and Z directions](https://community.mrtrix.org/t/extracting-fixels-along-the-x-y-and-z-directions/8727)
**Author:** [@Dr.quocvan](https://community.mrtrix.org/u/Dr.quocvan)\ **Replies:** 0\ **Last updated:** [March 24, 2026, 10:12am UTC](https://community.mrtrix.org/t/extracting-fixels-along-the-x-y-and-z-directions/8727 "2026-03-24T10:12:34Z")
Hi everyone, I have a question regarding extracting fixels along the X, Y, and Z directions. I followed the MRtrix3 reference documentation using fixel2sh and sh2peaks, but when visualizing with ODFs and fixel\_plot, the… --- ## [5ttgen fsl segmentation: GM misclassification in low contrast T1-region](https://community.mrtrix.org/t/5ttgen-fsl-segmentation-gm-misclassification-in-low-contrast-t1-region/8711)
**Author:** [@FEHildesheim](https://community.mrtrix.org/u/FEHildesheim)\ **Replies:** 1\ **Last updated:** [March 23, 2026, 2:39am UTC](https://community.mrtrix.org/t/5ttgen-fsl-segmentation-gm-misclassification-in-low-contrast-t1-region/8711 "2026-03-23T02:39:54Z")
Hello, I am running 5ttgen fsl using a brain-extracted T1 image that shows relatively low contrast in the circled area: I used 5ttgen fsl T1\_brain.nii.gz 5TT.nii.gz -premasked -nocrop The overall segmentation in T1… --- ## [DTI single shell 3T 32 directions dataset](https://community.mrtrix.org/t/dti-single-shell-3t-32-directions-dataset/8725)
**Author:** [@BenoitNoemie](https://community.mrtrix.org/u/BenoitNoemie)\ **Replies:** 0\ **Last updated:** [March 18, 2026, 1:23pm UTC](https://community.mrtrix.org/t/dti-single-shell-3t-32-directions-dataset/8725 "2026-03-18T13:23:14Z")
Hello everyone, I’m working with DTI data from schizophrenia patients (modalities in the title) and looking for the same dataset but for healthy/control subjects ? Looking for either the REC/PAR files or .nii ones in BI… --- ## [Prospects for 3.1.0 Release](https://community.mrtrix.org/t/prospects-for-3-1-0-release/8724)
**Author:** [@ejane.li](https://community.mrtrix.org/u/ejane.li)\ **Replies:** 0\ **Last updated:** [March 17, 2026, 4:52pm UTC](https://community.mrtrix.org/t/prospects-for-3-1-0-release/8724 "2026-03-17T16:52:28Z")
Hi MRtrix Team, Is there a timeline/plan for releasing version 3.1.0? Really hoping to use the kurtosis/dkt options (on centralised HPC clusters for lots of data). While the dev version is helpful, not ideal at present … --- ## [How to quantitatively compare two FOD reconstructions (subset reconstruction vs. full data)? — metrics & MRtrix commands](https://community.mrtrix.org/t/how-to-quantitatively-compare-two-fod-reconstructions-subset-reconstruction-vs-full-data-metrics-mrtrix-commands/8636)
**Author:** [@Oumayma\_Cherni](https://community.mrtrix.org/u/Oumayma_Cherni)\ **Replies:** 1\ **Last updated:** [March 17, 2026, 2:08am UTC](https://community.mrtrix.org/t/how-to-quantitatively-compare-two-fod-reconstructions-subset-reconstruction-vs-full-data-metrics-mrtrix-commands/8636 "2026-03-17T02:08:48Z")
Hello everyone, I have two FOD reconstructions from the same dataset: FOD\_A: reconstructed from a subset / alternative reconstruction (method X / fewer directions). FOD\_B: reconstructed from the complete original … --- ## [Question about pipeline structure and use of already co-registered T1 and DWI images Hello everyone, I am currently building a pipeline for tractography and connectome generation using MRtrix3, and I have a few questions regarding the correct workflow](https://community.mrtrix.org/t/question-about-pipeline-structure-and-use-of-already-co-registered-t1-and-dwi-images-hello-everyone-i-am-currently-building-a-pipeline-for-tractography-and-connectome-generation-using-mrtrix3-and-i-have-a-few-questions-regarding-the-correct-workflow/8721)
**Author:** [@Julia\_Falces\_Donoso](https://community.mrtrix.org/u/Julia_Falces_Donoso)\ **Replies:** 0\ **Last updated:** [March 11, 2026, 9:24am UTC](https://community.mrtrix.org/t/question-about-pipeline-structure-and-use-of-already-co-registered-t1-and-dwi-images-hello-everyone-i-am-currently-building-a-pipeline-for-tractography-and-connectome-generation-using-mrtrix3-and-i-have-a-few-questions-regarding-the-correct-workflow/8721 "2026-03-11T09:24:52Z")
Hello everyone, I am currently building a pipeline for tractography and connectome generation using MRtrix3, and I have a few questions regarding the correct workflow. First, I would like to confirm whether the process… --- ## [Generating orientation dispersion entropy](https://community.mrtrix.org/t/generating-orientation-dispersion-entropy/8718)
**Author:** [@Danny\_Kim](https://community.mrtrix.org/u/Danny_Kim)\ **Replies:** 0\ **Last updated:** [March 10, 2026, 6:59pm UTC](https://community.mrtrix.org/t/generating-orientation-dispersion-entropy/8718 "2026-03-10T18:59:08Z")
Hello fellow MRtrix3 users, I was wondering if anyone has experience in generating orientation dispersion entropy as mentioned by Enrico Kaden et al in 2016. I’ve read through the post in MRtrix3 discussion: Measure of… --- ## [Download and installation issues( Windows10)](https://community.mrtrix.org/t/download-and-installation-issues-windows10/8716)
**Author:** [@Chenchuang](https://community.mrtrix.org/u/Chenchuang)\ **Replies:** 1\ **Last updated:** [March 9, 2026, 10:38am UTC](https://community.mrtrix.org/t/download-and-installation-issues-windows10/8716 "2026-03-09T10:38:13Z")
--- ## [Deterministic tractography in MRtrix3](https://community.mrtrix.org/t/deterministic-tractography-in-mrtrix3/8652)
**Author:** [@Yuan\_Tao](https://community.mrtrix.org/u/Yuan_Tao)\ **Replies:** 3\ **Last updated:** [February 26, 2026, 9:10pm UTC](https://community.mrtrix.org/t/deterministic-tractography-in-mrtrix3/8652 "2026-02-26T21:10:06Z")
Dear MRTrix3 community, We did a connectome analysis with some rather old clinical data (b=700, 32 directions). I did FOD-based probability tractography with ACT, but got quite strong push back from reviewers and other … --- ## [Systematic FD offset between baseline and post-intervention timepoints in longitudinal FBA](https://community.mrtrix.org/t/systematic-fd-offset-between-baseline-and-post-intervention-timepoints-in-longitudinal-fba/8704)
**Author:** [@emmatinney](https://community.mrtrix.org/u/emmatinney)\ **Replies:** 0\ **Last updated:** [February 19, 2026, 4:02pm UTC](https://community.mrtrix.org/t/systematic-fd-offset-between-baseline-and-post-intervention-timepoints-in-longitudinal-fba/8704 "2026-02-19T16:02:09Z")
Hi all, I’m running a longitudinal fixel-based analysis on a large exercise intervention trial and I’m seeing a systematic increase in mean fiber density (FD) of approximately 0.1 at the post-intervention timepoint rela… --- ## [SS3T estimated WM in GM regions on infant scan w/ low b-value?](https://community.mrtrix.org/t/ss3t-estimated-wm-in-gm-regions-on-infant-scan-w-low-b-value/8702)
**Author:** [@tas923](https://community.mrtrix.org/u/tas923)\ **Replies:** 0\ **Last updated:** [February 19, 2026, 1:26am UTC](https://community.mrtrix.org/t/ss3t-estimated-wm-in-gm-regions-on-infant-scan-w-low-b-value/8702 "2026-02-19T01:26:07Z")
Hi everyone, I am very new to all of this and I am hoping to get some eyes on what I’ve got so far to make sure it looks correct. I am working with scans from 3-month old infants, b=700 in 30 directions, b=0 in 5 direct… --- ## [Phase encoding direction from Philips Achieva](https://community.mrtrix.org/t/phase-encoding-direction-from-philips-achieva/3578)
**Author:** [@jfhartzell](https://community.mrtrix.org/u/jfhartzell)\ **Replies:** 10\ **Last updated:** [February 18, 2026, 11:48pm UTC](https://community.mrtrix.org/t/phase-encoding-direction-from-philips-achieva/3578 "2026-02-18T23:48:08Z")
Hi I’d be grateful for some guidance in figuring out the correct phase-encoding directoin from a Philips Achieva 3T diffusion dataset. The dcm2niix .json file says “PhaseEncodingAxis”: “j”, “ImageOrientationPatientDI… --- ## [Diffusion spectrum imaging data for MSMT-CSD](https://community.mrtrix.org/t/diffusion-spectrum-imaging-data-for-msmt-csd/8691)
**Author:** [@anna\_de](https://community.mrtrix.org/u/anna_de)\ **Replies:** 1\ **Last updated:** [February 10, 2026, 6:50pm UTC](https://community.mrtrix.org/t/diffusion-spectrum-imaging-data-for-msmt-csd/8691 "2026-02-10T18:50:46Z")
Dear MRtrix3 Community, I am working with diffusion MRI data acquired using a diffusion spectrum imaging (DSI) sequence, 120 directions with a maximum b-value of 6,800 s/mm². We were able to preprocess the data successf… --- ## [Problem creating colour-coded DTI maps with MRtrix](https://community.mrtrix.org/t/problem-creating-colour-coded-dti-maps-with-mrtrix/3797)
**Author:** [@Claire](https://community.mrtrix.org/u/Claire)\ **Replies:** 5\ **Last updated:** [February 3, 2026, 9:55am UTC](https://community.mrtrix.org/t/problem-creating-colour-coded-dti-maps-with-mrtrix/3797 "2026-02-03T09:55:26Z")
Hi all, I’ve been having problems for some diffusion images when I run them through dwi2tensor and tensor2metric to create colour coded maps. The maps come out looking wrong: I have this problem when I convert the di… --- ## [Interpretation of TFNBS excel file](https://community.mrtrix.org/t/interpretation-of-tfnbs-excel-file/8689)
**Author:** [@Stephan](https://community.mrtrix.org/u/Stephan)\ **Replies:** 0\ **Last updated:** [February 3, 2026, 5:25am UTC](https://community.mrtrix.org/t/interpretation-of-tfnbs-excel-file/8689 "2026-02-03T05:25:50Z")
Hi Mrtrix3 community, I recently ran a TFNBS analysis on my diffusion MRI tractography based connectome using connectomestats, and I would like to ask a few clarifying questions. I am trying to assess group differences … --- ## [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… --- ## [Is it valid to mix single-tissue and multi-tissue FODs in population\_template?](https://community.mrtrix.org/t/is-it-valid-to-mix-single-tissue-and-multi-tissue-fods-in-population-template/8682)
**Author:** [@Zeyu](https://community.mrtrix.org/u/Zeyu)\ **Replies:** 1\ **Last updated:** [February 2, 2026, 9:26am UTC](https://community.mrtrix.org/t/is-it-valid-to-mix-single-tissue-and-multi-tissue-fods-in-population-template/8682 "2026-02-02T09:26:42Z")
Hello, I am designing a multi-center fixel-based analysis study. We have a practical challenge: Data from Site A was acquired with a single-shell protocol (b=2000 s/mm²). Data from Site B was acquired with a multi-she… --- ## [Fixel Based Analysis for lower b values?](https://community.mrtrix.org/t/fixel-based-analysis-for-lower-b-values/8686)
**Author:** [@hw009](https://community.mrtrix.org/u/hw009)\ **Replies:** 1\ **Last updated:** [February 2, 2026, 8:42am UTC](https://community.mrtrix.org/t/fixel-based-analysis-for-lower-b-values/8686 "2026-02-02T08:42:20Z")
Hello, I see in the Mrtrix documentation that it is recommended to do FBA with higher b values (\>2000 s/mm^2), but I see some clinical studies doing it with a b value of 1000 s/mm^2. Is the method reliable for lower b v… --- ## [CSD metrics for quality assurance for a large connectomics project](https://community.mrtrix.org/t/csd-metrics-for-quality-assurance-for-a-large-connectomics-project/8687)
**Author:** [@samuelholly](https://community.mrtrix.org/u/samuelholly)\ **Replies:** 0\ **Last updated:** [February 2, 2026, 8:11am UTC](https://community.mrtrix.org/t/csd-metrics-for-quality-assurance-for-a-large-connectomics-project/8687 "2026-02-02T08:11:25Z")
Dear MRtrix team, I would like to kindly ask for advice, but first some introduction. We would like to use MRtrix for a large connectomics project for which we recently received funding. We are planning to scan about 8… --- ## [Rationale for initial group-average in population\_template vs. external template](https://community.mrtrix.org/t/rationale-for-initial-group-average-in-population-template-vs-external-template/8681)
**Author:** [@Zeyu](https://community.mrtrix.org/u/Zeyu)\ **Replies:** 0\ **Last updated:** [January 28, 2026, 3:32am UTC](https://community.mrtrix.org/t/rationale-for-initial-group-average-in-population-template-vs-external-template/8681 "2026-01-28T03:32:02Z")
Hello, I am trying to understand the design philosophy behind the population\_template command’s initialization step. The documentation and common practice indicate that the algorithm starts by creating an initial avera… --- ## [Advice on Combining TBSS and ComBat](https://community.mrtrix.org/t/advice-on-combining-tbss-and-combat/8659)
**Author:** [@Miriam](https://community.mrtrix.org/u/Miriam)\ **Replies:** 0\ **Last updated:** [January 23, 2026, 12:49pm UTC](https://community.mrtrix.org/t/advice-on-combining-tbss-and-combat/8659 "2026-01-23T12:49:08Z")
Hello everyone, I’m looking for general recommendations on combining TBSS and ComBat when analyzing data from two sites (and three different scanners). Specifically, I’m unsure whether it’s better to: Harmonize the F… --- ## [DKI black voxels](https://community.mrtrix.org/t/dki-black-voxels/8657)
**Author:** [@Francesco](https://community.mrtrix.org/u/Francesco)\ **Replies:** 0\ **Last updated:** [January 19, 2026, 10:09am UTC](https://community.mrtrix.org/t/dki-black-voxels/8657 "2026-01-19T10:09:13Z")
Dear everyone, I am currently post-processing DKI data using MRtrix. After some trial and error, I managed to use the development pathway to compute the kurtosis metrics. This is my first experience working with these t… --- ## [Targeted Structural Connectivity Analysis](https://community.mrtrix.org/t/targeted-structural-connectivity-analysis/8640)
**Author:** [@rpampati](https://community.mrtrix.org/u/rpampati)\ **Replies:** 1\ **Last updated:** [January 17, 2026, 3:19pm UTC](https://community.mrtrix.org/t/targeted-structural-connectivity-analysis/8640 "2026-01-17T15:19:57Z")
Hello everyone, I am trying to conduct a structural connectivity analysis of the auditory pathway. I know that for full-brain structural connectivity, a tractogram is generated using ACT and the GM-WM interface, which i… --- ## [FBA template mask creation with subset of participants](https://community.mrtrix.org/t/fba-template-mask-creation-with-subset-of-participants/8331)
**Author:** [@LM10](https://community.mrtrix.org/u/LM10)\ **Replies:** 1\ **Last updated:** [January 9, 2026, 11:28am UTC](https://community.mrtrix.org/t/fba-template-mask-creation-with-subset-of-participants/8331 "2026-01-09T11:28:19Z")
I’m trying to run FBA on my muti-shell dataset of 600 patients and have a few questions about step 11 in the documentation (computing the template mask as the intersection of all subject masks in template space). The te… --- ## [The problem about the template mask in FBA](https://community.mrtrix.org/t/the-problem-about-the-template-mask-in-fba/8651)
**Author:** [@qianjinbo-creat](https://community.mrtrix.org/u/qianjinbo-creat)\ **Replies:** 0\ **Last updated:** [January 9, 2026, 2:52am UTC](https://community.mrtrix.org/t/the-problem-about-the-template-mask-in-fba/8651 "2026-01-09T02:52:27Z")
In the FBA analysis, I noticed that the group-space mask template generated by the command mrmath ${m} min ../group/template\_mask.mif -datatype bit is one circle smaller than the group-space FOD template. Later, I checke… --- ## [Update: Registration Open: IST Winter School 2026 (Hands-on Tractography) – Verona, Italy](https://community.mrtrix.org/t/update-registration-open-ist-winter-school-2026-hands-on-tractography-verona-italy/8648)
**Author:** [@Graham\_Little](https://community.mrtrix.org/u/Graham_Little)\ **Replies:** 0\ **Last updated:** [January 7, 2026, 8:11pm UTC](https://community.mrtrix.org/t/update-registration-open-ist-winter-school-2026-hands-on-tractography-verona-italy/8648 "2026-01-07T20:11:25Z")
Dear colleagues, We are pleased to announce that registration is now open for the IST Winter School 2026, organized by the International Society for Tractography. Dates: February 24–27, 2026 Location: University of Ver… [Previous page](https://community.mrtrix.org/latest.md?page=1) [Next page](https://community.mrtrix.org/latest.md?page=3)