# Uncategorized **URL:** https://community.mrtrix.org/c/uncategorized/1.md [Latest](https://community.mrtrix.org/latest.md) · [Categories](https://community.mrtrix.org/categories.md) · [Tags](https://community.mrtrix.org/tags.md) --- ## [Reposting: Dwi2response Dhollander: extreme SDM tails causing very small CSF candidate pools](https://community.mrtrix.org/t/reposting-dwi2response-dhollander-extreme-sdm-tails-causing-very-small-csf-candidate-pools/8836)
**Author:** [@WilliamFCB](https://community.mrtrix.org/u/WilliamFCB)\ **Replies:** 4\ **Last updated:** [September 19, 2026, 6:09am UTC](https://community.mrtrix.org/t/reposting-dwi2response-dhollander-extreme-sdm-tails-causing-very-small-csf-candidate-pools/8836 "2026-09-19T06:09:12Z")
I repost this as the the original post is greyed out and contains " preprocessing error", I did not get any response Hi MRtrix3 team, @ThijsDhollander @jdtournier I am investigating reproducible dwi2response dhollander… --- ## [Spurious group differences localized to the corticospinal tract in healthy control comparison: Protocol differences and CFE behavior at single-shell b=1000](https://community.mrtrix.org/t/spurious-group-differences-localized-to-the-corticospinal-tract-in-healthy-control-comparison-protocol-differences-and-cfe-behavior-at-single-shell-b-1000/8845)
**Author:** [@KazuoWashida](https://community.mrtrix.org/u/KazuoWashida)\ **Replies:** 1\ **Last updated:** [September 17, 2026, 3:35pm UTC](https://community.mrtrix.org/t/spurious-group-differences-localized-to-the-corticospinal-tract-in-healthy-control-comparison-protocol-differences-and-cfe-behavior-at-single-shell-b-1000/8845 "2026-09-17T15:35:09Z")
Hi MRtrix3 team and community, I am seeking advice regarding an unexpected finding during a Fixel-Based Analysis (FBA) comparing two cohorts of healthy controls. Context & Data We compared two independent cohorts of he… --- ## [Streamline assignment method for tractograms generated without ACT](https://community.mrtrix.org/t/streamline-assignment-method-for-tractograms-generated-without-act/8838)
**Author:** [@BrainzRCool](https://community.mrtrix.org/u/BrainzRCool)\ **Replies:** 0\ **Last updated:** [September 16, 2026, 6:35pm UTC](https://community.mrtrix.org/t/streamline-assignment-method-for-tractograms-generated-without-act/8838 "2026-09-16T18:35:48Z")
I ran tractography on our neonatal diffusion data. For the tckgen -mask argument, I used a liberal mask which includes the white matter, deep grey matter, cerebellum and brainstem. I did not use anatomically constrained … --- ## [Transforming fixel data from template space to native space](https://community.mrtrix.org/t/transforming-fixel-data-from-template-space-to-native-space/8835)
**Author:** [@Rishitha\_Praveen](https://community.mrtrix.org/u/Rishitha_Praveen)\ **Replies:** 0\ **Last updated:** [September 10, 2026, 6:30pm UTC](https://community.mrtrix.org/t/transforming-fixel-data-from-template-space-to-native-space/8835 "2026-09-10T18:30:41Z")
Dear MRtrix3 Team, I have a test.mif file containing fixel data in template space. The template-space image has dimenions of 486789 \* 1 \* 1 and a voxel size of 1.25 \*1.25 \* 1.25. The original native space DWI dimensions… --- ## [The direction of resampled tck file](https://community.mrtrix.org/t/the-direction-of-resampled-tck-file/7643)
**Author:** [@Yuheng](https://community.mrtrix.org/u/Yuheng)\ **Replies:** 1\ **Last updated:** [September 10, 2026, 1:29pm UTC](https://community.mrtrix.org/t/the-direction-of-resampled-tck-file/7643 "2026-09-10T13:29:12Z")
Hi, I am currently running ROI to ROI tractography and want to fit the FA map onto the tracts, just like this Resampling. I generated tracts from LGN to V1 and from V1 to LGN using tckgen, and then the two tck files we… --- ## [dwidenoise applied to complex data](https://community.mrtrix.org/t/dwidenoise-applied-to-complex-data/6546)
**Author:** [@josepman](https://community.mrtrix.org/u/josepman)\ **Replies:** 5\ **Last updated:** [September 2, 2026, 6:57am UTC](https://community.mrtrix.org/t/dwidenoise-applied-to-complex-data/6546 "2026-09-02T06:57:47Z")
Hi, I have phase and magnitude data acquired with a Siemens PRISMA scanner at a reasonably low SNR. I tried applying dwidenoise in the complex data but I am not sure it is performing better. For instance, I can see the … --- ## [Fixel processing in marmoset brain images](https://community.mrtrix.org/t/fixel-processing-in-marmoset-brain-images/8824)
**Author:** [@bigaddo81](https://community.mrtrix.org/u/bigaddo81)\ **Replies:** 0\ **Last updated:** [September 2, 2026, 6:23am UTC](https://community.mrtrix.org/t/fixel-processing-in-marmoset-brain-images/8824 "2026-09-02T06:23:30Z")
Mrtrix developers, I have in-vivo, multishell marmoset data that I want to perform an FBA on. I have manual segmentations of the WM and GM voxels in all specimens and have done msmt FOD estimation. The WM FODs in the p… --- ## [Along tract analysis after tract segmentation](https://community.mrtrix.org/t/along-tract-analysis-after-tract-segmentation/1007)
**Author:** [@Frederike](https://community.mrtrix.org/u/Frederike)\ **Replies:** 8\ **Last updated:** [September 1, 2026, 7:45pm UTC](https://community.mrtrix.org/t/along-tract-analysis-after-tract-segmentation/1007 "2026-09-01T19:45:50Z")
Dear experts, I am a relatively new user of MRtrix 3 and would be therefore highly thankful for your help and support: I performed automatized preprocessing (dwi2preproc etc.) and wholebrain-tractography (tckgen). Afte… --- ## [Connectivity-based parcellation from an existing GPe–STN tractogram: voxel-wise fingerprints and Ward clustering](https://community.mrtrix.org/t/connectivity-based-parcellation-from-an-existing-gpe-stn-tractogram-voxel-wise-fingerprints-and-ward-clustering/8821)
**Author:** [@nicolas.tempier](https://community.mrtrix.org/u/nicolas.tempier)\ **Replies:** 0\ **Last updated:** [August 31, 2026, 8:18am UTC](https://community.mrtrix.org/t/connectivity-based-parcellation-from-an-existing-gpe-stn-tractogram-voxel-wise-fingerprints-and-ward-clustering/8821 "2026-08-31T08:18:41Z")
Hi MRtrix community, We are currently performing an exploratory connectivity-based parcellation of the STN from an existing GPe–STN tractogram, as part of a revision of a manuscript. The aim is to determine whether the… --- ## [Filter streamlines by endpoint landing ROIs](https://community.mrtrix.org/t/filter-streamlines-by-endpoint-landing-rois/8817)
**Author:** [@jhlegarreta](https://community.mrtrix.org/u/jhlegarreta)\ **Replies:** 1\ **Last updated:** [August 26, 2026, 1:24am UTC](https://community.mrtrix.org/t/filter-streamlines-by-endpoint-landing-rois/8817 "2026-08-26T01:24:25Z")
Hi folks, I would like to make sure that the below usage of tckedit answers the following problem: having a tractogram that has been seeded from a region in the GMWMI, I am trying to find the streamlines that connect a … --- ## [Streamlines produced by ACT expected to start/end in the GM?](https://community.mrtrix.org/t/streamlines-produced-by-act-expected-to-start-end-in-the-gm/8816)
**Author:** [@jhlegarreta](https://community.mrtrix.org/u/jhlegarreta)\ **Replies:** 0\ **Last updated:** [August 18, 2026, 6:25am UTC](https://community.mrtrix.org/t/streamlines-produced-by-act-expected-to-start-end-in-the-gm/8816 "2026-08-18T06:25:50Z")
Hi, I am trying to understand the effect of tckgen (called with iFDOD2+ACT) and tckedit. Am I understanding correctly that tckgen called with iFDOD2+ACT, e.g. tckgen \\ -algorithm ifod2 \\ -act "${5ttgen\_fname}" \\ … --- ## [Can a fixed number of streamlines be generated with \`seed\_grid\_per\_voxel\`?](https://community.mrtrix.org/t/can-a-fixed-number-of-streamlines-be-generated-with-seed-grid-per-voxel/8815)
**Author:** [@jhlegarreta](https://community.mrtrix.org/u/jhlegarreta)\ **Replies:** 0\ **Last updated:** [August 18, 2026, 6:21am UTC](https://community.mrtrix.org/t/can-a-fixed-number-of-streamlines-be-generated-with-seed-grid-per-voxel/8815 "2026-08-18T06:21:58Z")
Hi folks, thanks for putting together and maintaining MRTrix. I am trying to use tckgen using iFOD2 with ACT to get some tractography data. I am trying to seed a particular region of the whole-brain GMWMI, and I have … --- ## [Fixel-based analysis with two visits: 64 vs 128 directions at b=1000 – should I downsample?](https://community.mrtrix.org/t/fixel-based-analysis-with-two-visits-64-vs-128-directions-at-b-1000-should-i-downsample/8814)
**Author:** [@hw009](https://community.mrtrix.org/u/hw009)\ **Replies:** 0\ **Last updated:** [August 17, 2026, 1:51pm UTC](https://community.mrtrix.org/t/fixel-based-analysis-with-two-visits-64-vs-128-directions-at-b-1000-should-i-downsample/8814 "2026-08-17T13:51:25Z")
I have diffusion MRI data at b=1000 s/mm² acquired at two visits. Visit 1 used 64 diffusion-encoding directions, while visit 2 used 128 directions. I’m planning to perform fixel-based analysis (FBA) on this longitudinal … --- ## [Tcksift2 returns NaN proportionality coefficient and unit weights for one ODF dataset](https://community.mrtrix.org/t/tcksift2-returns-nan-proportionality-coefficient-and-unit-weights-for-one-odf-dataset/8813)
**Author:** [@Maksym](https://community.mrtrix.org/u/Maksym)\ **Replies:** 0\ **Last updated:** [August 13, 2026, 9:49pm UTC](https://community.mrtrix.org/t/tcksift2-returns-nan-proportionality-coefficient-and-unit-weights-for-one-odf-dataset/8813 "2026-08-13T21:49:22Z")
Hi everyone, I’m having an issue with tcksift2 for one of my weekly ODF datasets and would appreciate some help understanding where the problem comes from. I have a series of weekly ODF files (weeks 32-44 from developin… --- ## [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… --- ## [NaN values in FA Map](https://community.mrtrix.org/t/nan-values-in-fa-map/8806)
**Author:** [@nschalkx](https://community.mrtrix.org/u/nschalkx)\ **Replies:** 0\ **Last updated:** [August 3, 2026, 9:20am UTC](https://community.mrtrix.org/t/nan-values-in-fa-map/8806 "2026-08-03T09:20:14Z")
I have created some FA maps using the MRTrix suite, but after closer inspection of the images there are multiple ‘holes’ in the map, where the value is NaN / ?. I have attached some screenshots of the ‘holes’ in question… --- ## [Slow dwiconvert on HCP data](https://community.mrtrix.org/t/slow-dwiconvert-on-hcp-data/8803)
**Author:** [@antoniodm](https://community.mrtrix.org/u/antoniodm)\ **Replies:** 0\ **Last updated:** [August 2, 2026, 10:32am UTC](https://community.mrtrix.org/t/slow-dwiconvert-on-hcp-data/8803 "2026-08-02T10:32:23Z")
Hello! I’ve been using MRtrix for a while. Lately I’ve noticed that commands like dwi2response and dwi2fod spend an unexpectedly long time just getting the data into memory. Watching the process, nearly all the wall-clo… --- ## [Conda installation for mrtrix3](https://community.mrtrix.org/t/conda-installation-for-mrtrix3/8791)
**Author:** [@AliceJ](https://community.mrtrix.org/u/AliceJ)\ **Replies:** 5\ **Last updated:** [July 2, 2026, 4:28pm UTC](https://community.mrtrix.org/t/conda-installation-for-mrtrix3/8791 "2026-07-02T16:28:09Z")
Hello all ! I have a question regarding the conda installation for mrtrix3. Since 2024 Anaconda updated their Terms of Service and access to community-hosted channels on anaconda.org is now restricted for users connect… --- ## [Seeding from the thalamus](https://community.mrtrix.org/t/seeding-from-the-thalamus/1488)
**Author:** [@cbajada](https://community.mrtrix.org/u/cbajada)\ **Replies:** 5\ **Last updated:** [June 27, 2026, 5:46pm UTC](https://community.mrtrix.org/t/seeding-from-the-thalamus/1488 "2026-06-27T17:46:39Z")
Hi all, I’d like to run an experiment seeding from the thalamus but am concerned about the effect of ACT. What do you suggest? I was thinking of removing the thalamus (and possibly the rest of the deep GM) from the GM … --- ## [Handling FA values \> 1 before voxel-wise TFCE analysis](https://community.mrtrix.org/t/handling-fa-values-1-before-voxel-wise-tfce-analysis/8792)
**Author:** [@diana\_99](https://community.mrtrix.org/u/diana_99)\ **Replies:** 0\ **Last updated:** [June 25, 2026, 3:05pm UTC](https://community.mrtrix.org/t/handling-fa-values-1-before-voxel-wise-tfce-analysis/8792 "2026-06-25T15:05:51Z")
Hello everyone, I am fitting the diffusion tensor with MRtrix3 and have found a small number of voxels with FA values greater than 1. In every voxel where FA \> 1, one of the tensor eigenvalues is negative. The affected… --- ## [Building tractography pipeline](https://community.mrtrix.org/t/building-tractography-pipeline/8739)
**Author:** [@adambaker](https://community.mrtrix.org/u/adambaker)\ **Replies:** 4\ **Last updated:** [June 24, 2026, 7:00pm UTC](https://community.mrtrix.org/t/building-tractography-pipeline/8739 "2026-06-24T19:00:47Z")
Hi MRTrix team, I am building my analysis pipeline and am curious your thoughts on my approach. My data are b=0,1000,2000. I would like to implement ACT via 5ttgen. I initially attempted 5ttgen fsl, which worked for a … --- ## [Template\_mask in FBA](https://community.mrtrix.org/t/template-mask-in-fba/8787)
**Author:** [@qianjinbo-creat](https://community.mrtrix.org/u/qianjinbo-creat)\ **Replies:** 2\ **Last updated:** [June 23, 2026, 3:00am UTC](https://community.mrtrix.org/t/template-mask-in-fba/8787 "2026-06-23T03:00:48Z")
In FBA analysis, should the template\_mask be generated using the masks of subjects that created the wmfod\_template, or the masks of all subjects?Thank you --- ## [Two-shell acquisition for MSMT-CSD protocol recommendation?](https://community.mrtrix.org/t/two-shell-acquisition-for-msmt-csd-protocol-recommendation/8785)
**Author:** [@Sebastian\_Navarrete](https://community.mrtrix.org/u/Sebastian_Navarrete)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 3:10pm UTC](https://community.mrtrix.org/t/two-shell-acquisition-for-msmt-csd-protocol-recommendation/8785 "2026-06-10T15:10:31Z")
Hi MRtrix3 experts, For the past years we have been acquiring single-shell data, but we now want to improve our DWI acquisition in order to use MSMT-CSD correctly. I searched for multi-shell acquisition references and… --- ## [How to practically apply SIFT2 mu to structural connectomes?](https://community.mrtrix.org/t/how-to-practically-apply-sift2-mu-to-structural-connectomes/8385)
**Author:** [@mab7899](https://community.mrtrix.org/u/mab7899)\ **Replies:** 1\ **Last updated:** [June 5, 2026, 5:12pm UTC](https://community.mrtrix.org/t/how-to-practically-apply-sift2-mu-to-structural-connectomes/8385 "2026-06-05T17:12:22Z")
I am generating subject-level structural connectomes based on the recently published Nature Protocol (Structural connectome construction using constrained spherical deconvolution in multi-shell diffusion-weighted magneti… --- ## [Robust cross-modality neonatal atlas registration (T1w template → T2w subject)](https://community.mrtrix.org/t/robust-cross-modality-neonatal-atlas-registration-t1w-template-t2w-subject/8782)
**Author:** [@anchalbhaskar](https://community.mrtrix.org/u/anchalbhaskar)\ **Replies:** 2\ **Last updated:** [June 1, 2026, 2:46pm UTC](https://community.mrtrix.org/t/robust-cross-modality-neonatal-atlas-registration-t1w-template-t2w-subject/8782 "2026-06-01T14:46:04Z")
Hi all, I am building structural connectomes for preterm neonates (dHCP data, SHARD-preprocessed dMRI) using the MRtrix3 MSMT-CSD → ACT → SIFT2 → \`tck2connectome\` workflow (following Tahedl, Tournier & Smith 2025). Trac… --- ## [Prepocessing phantom data](https://community.mrtrix.org/t/prepocessing-phantom-data/8777)
**Author:** [@philippedionne](https://community.mrtrix.org/u/philippedionne)\ **Replies:** 0\ **Last updated:** [May 28, 2026, 6:57pm UTC](https://community.mrtrix.org/t/prepocessing-phantom-data/8777 "2026-05-28T18:57:16Z")
Hi all, I’m having a problem while running the dwifslpreproc command on DWI volumes acquired on phantom data. The data consist of 3 runs of the same acquisition protocol (33 volumes each, with 6 b0s acquired in AP direc… --- ## [NODDI-like metrics from single-shell DWI](https://community.mrtrix.org/t/noddi-like-metrics-from-single-shell-dwi/8774)
**Author:** [@diana\_99](https://community.mrtrix.org/u/diana_99)\ **Replies:** 0\ **Last updated:** [May 24, 2026, 2:41pm UTC](https://community.mrtrix.org/t/noddi-like-metrics-from-single-shell-dwi/8774 "2026-05-24T14:41:50Z")
Hello everyone, I am working with a dataset that is single-shell DWI. I know that standard NODDI is designed for multi-shell DWI, so I wanted to ask if there are any methods for estimating NODDI-like metrics from single… --- ## [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… [Next page](https://community.mrtrix.org/c/uncategorized/1.md?page=1)