# Latest **URL:** https://community.mrtrix.org/latest.md?page=1 [Latest](https://community.mrtrix.org/latest.md) · [Categories](https://community.mrtrix.org/categories.md) · [Tags](https://community.mrtrix.org/tags.md) **Page:** 2 --- ## [SIAM: AI brain segmentation model](https://community.mrtrix.org/t/siam-ai-brain-segmentation-model/8771)
**Author:** [@Romain\_Valabregue](https://community.mrtrix.org/u/Romain_Valabregue)\ **Replies:** 0\ **Last updated:** [May 21, 2026, 10:21am UTC](https://community.mrtrix.org/t/siam-ai-brain-segmentation-model/8771 "2026-05-21T10:21:22Z")
Hi there For those who are not satisfy by freesurfer (or fassurfer) segmentation (for intance the putamen is systematically a part of the claustrum), give a try to SIAM Current version is performing only tissue segment… --- ## [Fixelcfetstats: no streamlines connectivitiy for some fixels](https://community.mrtrix.org/t/fixelcfetstats-no-streamlines-connectivitiy-for-some-fixels/8758)
**Author:** [@iqraalimirza16](https://community.mrtrix.org/u/iqraalimirza16)\ **Replies:** 1\ **Last updated:** [May 21, 2026, 5:54am UTC](https://community.mrtrix.org/t/fixelcfetstats-no-streamlines-connectivitiy-for-some-fixels/8758 "2026-05-21T05:54:17Z")
Hey all, I completed steps for the whole brain FBA following this tutorial: Fibre density and cross-section - Multi-tissue CSD — MRtrix3 3.0 documentation While running fixelcfestats I get this warning which I am uns… --- ## [For FBA analysis](https://community.mrtrix.org/t/for-fba-analysis/8769)
**Author:** [@qianjinbo-creat](https://community.mrtrix.org/u/qianjinbo-creat)\ **Replies:** 2\ **Last updated:** [May 21, 2026, 4:54am UTC](https://community.mrtrix.org/t/for-fba-analysis/8769 "2026-05-21T04:54:54Z")
Some cerebellar DTI scans are complete while others are incomplete. Will this affect the cerebral FBA analysis? --- ## [Neonatal WM atlas](https://community.mrtrix.org/t/neonatal-wm-atlas/3244)
**Author:** [@ros](https://community.mrtrix.org/u/ros)\ **Replies:** 22\ **Last updated:** [May 20, 2026, 10:23am UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244 "2026-05-20T10:23:55Z")
I would like to define ROIs of WM tracts in a neonatal image of brain. I have 3dT1 and DKI scan. I should use 3dT1 as an anatomical reference. Do you suggest any existing neonatal atlas to do so? thank you. Here you fi… --- ## [Fixel2voxel dimension mismatch](https://community.mrtrix.org/t/fixel2voxel-dimension-mismatch/8753)
**Author:** [@marcelzwiers](https://community.mrtrix.org/u/marcelzwiers)\ **Replies:** 4\ **Last updated:** [May 14, 2026, 5:12pm UTC](https://community.mrtrix.org/t/fixel2voxel-dimension-mismatch/8753 "2026-05-14T17:12:44Z")
Hi all, I’m new to MRtrix, so I hope my issue can be addressed easily (due to my misunderstanding). I ran into the following issue: I have MRtrix FOD data, as generated by qsiprep. I segmented the FOD to fixels with: $… --- ## [The tractography trajectories from mouse dMRI do not match the projection pathways visualized by high-titer viral tracing](https://community.mrtrix.org/t/the-tractography-trajectories-from-mouse-dmri-do-not-match-the-projection-pathways-visualized-by-high-titer-viral-tracing/8755)
**Author:** [@fengmingqin1](https://community.mrtrix.org/u/fengmingqin1)\ **Replies:** 1\ **Last updated:** [May 12, 2026, 2:02am UTC](https://community.mrtrix.org/t/the-tractography-trajectories-from-mouse-dmri-do-not-match-the-projection-pathways-visualized-by-high-titer-viral-tracing/8755 "2026-05-12T02:02:51Z")
"The dMRI tractography trajectories in mice do not align with the projective pathways visualized by high-titer viral tracing. I have attempted various parameter combinations, but the discrepancies remain significant. The… --- ## [Cluster threshold when visualising fixel plots](https://community.mrtrix.org/t/cluster-threshold-when-visualising-fixel-plots/5058)
**Author:** [@zito](https://community.mrtrix.org/u/zito)\ **Replies:** 5\ **Last updated:** [May 3, 2026, 1:39pm UTC](https://community.mrtrix.org/t/cluster-threshold-when-visualising-fixel-plots/5058 "2026-05-03T13:39:26Z")
Hello dear MRtrix community, I am wondering whether mrview has a function to display only fixels which clusters above a certain threshold. To be more precise, in SPM-fMRI you can filter out single voxels of activity be… --- ## [Connectomestats to compare groups](https://community.mrtrix.org/t/connectomestats-to-compare-groups/8357)
**Author:** [@diana\_99](https://community.mrtrix.org/u/diana_99)\ **Replies:** 8\ **Last updated:** [April 25, 2026, 11:01am UTC](https://community.mrtrix.org/t/connectomestats-to-compare-groups/8357 "2026-04-25T11:01:51Z")
Hello everyone, I am starting my analysis with connectomestats and I would like to compare connectomes from the same subjects at two time points, and also compare these with controls, separately. I suppose I need to per… --- ## [Extracting only tracts from significant fixels?](https://community.mrtrix.org/t/extracting-only-tracts-from-significant-fixels/8496)
**Author:** [@Ivan\_Campbell](https://community.mrtrix.org/u/Ivan_Campbell)\ **Replies:** 4\ **Last updated:** [April 22, 2026, 1:04pm UTC](https://community.mrtrix.org/t/extracting-only-tracts-from-significant-fixels/8496 "2026-04-22T13:04:26Z")
I’ve recently completed an FDC stats analysis and I’m trying to find a way to automatically identify the significant tracts. I’m unaware of any way to do this natively in MRtrix (please correct me if there is), so I’m ho… --- ## [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… --- ## [Template Mask Creation Issue](https://community.mrtrix.org/t/template-mask-creation-issue/8751)
**Author:** [@almatuschak](https://community.mrtrix.org/u/almatuschak)\ **Replies:** 1\ **Last updated:** [April 22, 2026, 12:32pm UTC](https://community.mrtrix.org/t/template-mask-creation-issue/8751 "2026-04-22T12:32:44Z")
Hi! I have a problem with creating the template mask for FBA. My template mask excludes a part of the brain. This, of course, results in my fixel mask also missing this part. I already excluded 3 participants who had pa… --- ## [Label lookup files for Lausanne + THOMAS parcellation combination](https://community.mrtrix.org/t/label-lookup-files-for-lausanne-thomas-parcellation-combination/8750)
**Author:** [@Free\_Surfer](https://community.mrtrix.org/u/Free_Surfer)\ **Replies:** 2\ **Last updated:** [April 16, 2026, 7:50pm UTC](https://community.mrtrix.org/t/label-lookup-files-for-lausanne-thomas-parcellation-combination/8750 "2026-04-16T19:50:18Z")
Hello, I’m recreating the pipeline from the paper (https://onlinelibrary.wiley.com/doi/10.1002/epi.70099) and am currently attempting to combine Lausanne and THOAMS parcellations, but can’t seem to find some crucial fil… --- ## [FBA analysis pipeline help](https://community.mrtrix.org/t/fba-analysis-pipeline-help/1276)
**Author:** [@Kar](https://community.mrtrix.org/u/Kar)\ **Replies:** 47\ **Last updated:** [April 13, 2026, 11:25pm UTC](https://community.mrtrix.org/t/fba-analysis-pipeline-help/1276 "2026-04-13T23:25:57Z")
Hi, I am performing FBA using warps generated from ANTS using the instructions: https://community.mrtrix.org/t/registration-using-transformations-generated-from-other-packages/2259 I want to apply FOD modulation during… --- ## [Understanding Extracted Vals](https://community.mrtrix.org/t/understanding-extracted-vals/8744)
**Author:** [@Ienwesi](https://community.mrtrix.org/u/Ienwesi)\ **Replies:** 0\ **Last updated:** [April 13, 2026, 10:21pm UTC](https://community.mrtrix.org/t/understanding-extracted-vals/8744 "2026-04-13T22:21:09Z")
Hello! Quite newer to the neuro world and have a few questions. I had GQI streamlines for infant brains for my ROIs and then model-tensor dwi maps all done through DSI studio. I then used tcksample to extract mean FAs, … --- ## [Libtiff.so.5 not found in Ubuntu Lunar Lobster 23.04](https://community.mrtrix.org/t/libtiff-so-5-not-found-in-ubuntu-lunar-lobster-23-04/6837)
**Author:** [@Alexandre](https://community.mrtrix.org/u/Alexandre)\ **Replies:** 4\ **Last updated:** [April 13, 2026, 8:39pm UTC](https://community.mrtrix.org/t/libtiff-so-5-not-found-in-ubuntu-lunar-lobster-23-04/6837 "2026-04-13T20:39:48Z")
Ubuntu 23.04 ships with libtiff.so.6 and libtiff.so.5 doesn’t seem to be available. I’ve installed MRtrix3 throught anaconda and have used a workaround to make it work by creating a symbolic link to version 6 with the fo… --- ## [Missing peaks with sh2peaks](https://community.mrtrix.org/t/missing-peaks-with-sh2peaks/8732)
**Author:** [@daducci](https://community.mrtrix.org/u/daducci)\ **Replies:** 8\ **Last updated:** [April 13, 2026, 4:11pm UTC](https://community.mrtrix.org/t/missing-peaks-with-sh2peaks/8732 "2026-04-13T16:11:34Z")
Hi guys, I’m trying to compute peaks from an SH function with two very clear/distinct lobes (see screenshot #1), but sometimes major peaks are missed in place of much smaller ones (see screenshot #2). The SH functions w… --- ## [T Value Map](https://community.mrtrix.org/t/t-value-map/8741)
**Author:** [@H.A.N.K](https://community.mrtrix.org/u/H.A.N.K)\ **Replies:** 0\ **Last updated:** [April 13, 2026, 12:01am UTC](https://community.mrtrix.org/t/t-value-map/8741 "2026-04-13T00:01:21Z")
Hi All, I used TractSeg to extract a fixel mask for my tract of interest, and when examining the resulting t-value map, I was uncertain which value should be interpreted as the actual “t value,” given that the map is pr… --- ## [Position of -nthreads N in for\_each command](https://community.mrtrix.org/t/position-of-nthreads-n-in-for-each-command/8740)
**Author:** [@almatuschak](https://community.mrtrix.org/u/almatuschak)\ **Replies:** 0\ **Last updated:** [April 10, 2026, 8:01pm UTC](https://community.mrtrix.org/t/position-of-nthreads-n-in-for-each-command/8740 "2026-04-10T20:01:18Z")
Hi! I was looking at the MRtrix wiki for batch processing ( Batch processing with for\_each — MRtrix3 3.0 documentation ) and found that it says the following: Indeed these two usages can in theory be combined. Imagine t… --- ## [Matching of sample for template creation](https://community.mrtrix.org/t/matching-of-sample-for-template-creation/8736)
**Author:** [@iqraalimirza16](https://community.mrtrix.org/u/iqraalimirza16)\ **Replies:** 0\ **Last updated:** [April 10, 2026, 1:36pm UTC](https://community.mrtrix.org/t/matching-of-sample-for-template-creation/8736 "2026-04-10T13:36:34Z")
Hi all! For my Master’s thesis I am doing a fixel-based analysis and I am at the template creation step. My population includes people with and without evidence of coronary artery calcification (CAC) so high vs absent CA… --- ## [FBA - problems with masks](https://community.mrtrix.org/t/fba-problems-with-masks/8717)
**Author:** [@katoherregods](https://community.mrtrix.org/u/katoherregods)\ **Replies:** 4\ **Last updated:** [April 9, 2026, 3:14pm UTC](https://community.mrtrix.org/t/fba-problems-with-masks/8717 "2026-04-09T15:14:31Z")
Hi Mrtrixers! For my master thesis, I am performing the MSMT-FBA analysis exactly as described in Mrtrix-readthedocs, but I noticed that my masks include a LOT of non-brain regions. This is the case for both my binary… --- ## [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… [Previous page](https://community.mrtrix.org/latest.md) [Next page](https://community.mrtrix.org/latest.md?page=2)