# \#tractography **URL:** https://community.mrtrix.org/tag/tractography/14.md [Latest](https://community.mrtrix.org/latest.md) · [Categories](https://community.mrtrix.org/categories.md) · [Tags](https://community.mrtrix.org/tags.md) --- ## [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:** 2\ **Last updated:** [September 29, 2026, 8:16am UTC](https://community.mrtrix.org/t/filter-streamlines-by-endpoint-landing-rois/8817 "2026-09-29T08:16:41Z")
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 … --- ## [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… --- ## [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 … --- ## [Can we use two different seed options to generate 5M streamlines contributed from each option](https://community.mrtrix.org/t/can-we-use-two-different-seed-options-to-generate-5m-streamlines-contributed-from-each-option/8768)
**Author:** [@suhail](https://community.mrtrix.org/u/suhail)\ **Replies:** 4\ **Last updated:** [July 28, 2026, 3:37pm UTC](https://community.mrtrix.org/t/can-we-use-two-different-seed-options-to-generate-5m-streamlines-contributed-from-each-option/8768 "2026-07-28T15:37:28Z")
Dear Experts, Command : tckgen -act 5tt\_coreg.mif -backtrack \\ $wmFOD $tckFName -seed\_gmwmi gmwmi.mif -seed\_image maskImage.nii.gz -select 10M -cutoff 0.05 --force Queries : 1.Can we use two different seed options … --- ## [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 … --- ## [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… --- ## [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… --- ## [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? --- ## [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 … --- ## [Fiber tracts for corpus callosum](https://community.mrtrix.org/t/fiber-tracts-for-corpus-callosum/8635)
**Author:** [@hirak](https://community.mrtrix.org/u/hirak)\ **Replies:** 2\ **Last updated:** [December 12, 2025, 10:29pm UTC](https://community.mrtrix.org/t/fiber-tracts-for-corpus-callosum/8635 "2025-12-12T22:29:26Z")
Greetings. I want to fiber tractography using mrtrix. I am specifically interested in visualizing corpus callosum tracts. I want to compare the tracts for visualization (ground truth tracts for b = 2000 shell data from t… --- ## [Probabilistic tractography on high-res dMRI data not providing good enough results](https://community.mrtrix.org/t/probabilistic-tractography-on-high-res-dmri-data-not-providing-good-enough-results/8632)
**Author:** [@jhlegarreta](https://community.mrtrix.org/u/jhlegarreta)\ **Replies:** 1\ **Last updated:** [December 12, 2025, 10:22pm UTC](https://community.mrtrix.org/t/probabilistic-tractography-on-high-res-dmri-data-not-providing-good-enough-results/8632 "2025-12-12T22:22:35Z")
Hi MRtrix crew, thanks for developing and maintaining the tool. I am trying to perform probabilistic tractography on an in-house high-res (0.7 mm iso; b=1000 s/mm2; 60 directions plus 1 b0) dMRI dataset. I am using iFO… --- ## [Transform tractography outputs to a .nii file](https://community.mrtrix.org/t/transform-tractography-outputs-to-a-nii-file/8623)
**Author:** [@Chai](https://community.mrtrix.org/u/Chai)\ **Replies:** 1\ **Last updated:** [November 26, 2025, 10:42am UTC](https://community.mrtrix.org/t/transform-tractography-outputs-to-a-nii-file/8623 "2025-11-26T10:42:02Z")
Dear experts, I have utilized MRtrix and tractography toolbox TractSeg to reconstruct 72 white matter tracts for each subject. I want to transform the tractography output .tck file of each tract to .nii file, and I am n… --- ## [Whole-brain tck to MNI](https://community.mrtrix.org/t/whole-brain-tck-to-mni/8611)
**Author:** [@fhaos123](https://community.mrtrix.org/u/fhaos123)\ **Replies:** 1\ **Last updated:** [November 18, 2025, 4:36am UTC](https://community.mrtrix.org/t/whole-brain-tck-to-mni/8611 "2025-11-18T04:36:03Z")
Hi Mrtrix community, We tried to register the whole-brain tractogram to MNI space, but some problems appeared. We noticed that the tck files already warped to MNI space are misaligned with the standard template in some… --- ## [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’,… --- ## [Conversion of streamlines from trk to tck](https://community.mrtrix.org/t/conversion-of-streamlines-from-trk-to-tck/806)
**Author:** [@sharon](https://community.mrtrix.org/u/sharon)\ **Replies:** 21\ **Last updated:** [October 29, 2025, 4:16pm UTC](https://community.mrtrix.org/t/conversion-of-streamlines-from-trk-to-tck/806 "2025-10-29T16:16:35Z")
Dear all, I am currently working on DSI tracking. I use Dipy to generate the spherical harmonics and then doing a tracking giving a .trk file. Then, I would like to convert it into .tck to be able to use it with MRtri… --- ## [ACT for leg muscles instead of brain tissue](https://community.mrtrix.org/t/act-for-leg-muscles-instead-of-brain-tissue/8512)
**Author:** [@namrauf](https://community.mrtrix.org/u/namrauf)\ **Replies:** 2\ **Last updated:** [September 10, 2025, 3:03pm UTC](https://community.mrtrix.org/t/act-for-leg-muscles-instead-of-brain-tissue/8512 "2025-09-10T15:03:42Z")
Hi, I would like to know if we can do Anatomically constrained tractography (ACT) for non-brain tissue i.e. muscles of leg. I have the T1 scan, segmented muscles and tendons mask and have already coregistered them to t… --- ## [Why does tckconvert create a mismatch?](https://community.mrtrix.org/t/why-does-tckconvert-create-a-mismatch/8507)
**Author:** [@Zifei\_Liang](https://community.mrtrix.org/u/Zifei_Liang)\ **Replies:** 1\ **Last updated:** [September 7, 2025, 11:24am UTC](https://community.mrtrix.org/t/why-does-tckconvert-create-a-mismatch/8507 "2025-09-07T11:24:54Z")
I used tckconvert -scanner2voxel convert the tck to voxel space. But after process, I found the MRI image and fibers are not matched anymore. My initial MRI image T1.nii is 1.25x1.25x1.25mm isotropic, and matched fib… --- ## [Tckgen -seed\_image option for fiber tracking](https://community.mrtrix.org/t/tckgen-seed-image-option-for-fiber-tracking/8490)
**Author:** [@Isaac\_Prentiss](https://community.mrtrix.org/u/Isaac_Prentiss)\ **Replies:** 0\ **Last updated:** [August 16, 2025, 6:34pm UTC](https://community.mrtrix.org/t/tckgen-seed-image-option-for-fiber-tracking/8490 "2025-08-16T18:34:03Z")
Hi all, I’m still a bit new to tractography, so I apologize if my uncertainty is a bit naive. I’m working on a project comparing the performance of different diffusion MRI signal models (specifically DTI and free water … --- ## [Tckgen -maxlength value for interhemispheric connections](https://community.mrtrix.org/t/tckgen-maxlength-value-for-interhemispheric-connections/7447)
**Author:** [@wneaves](https://community.mrtrix.org/u/wneaves)\ **Replies:** 1\ **Last updated:** [August 4, 2025, 6:59pm UTC](https://community.mrtrix.org/t/tckgen-maxlength-value-for-interhemispheric-connections/7447 "2025-08-04T18:59:02Z")
Hi all, I’m somewhat of a novice with fiber tracking, looking for a bit of help. I understand that the default value for tckgen is 100 \* voxel size. When investigating interhemispheric connections, this understandably … --- ## [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 … --- ## [Clarification on tckmap TDI contrast behavior](https://community.mrtrix.org/t/clarification-on-tckmap-tdi-contrast-behavior/8430)
**Author:** [@Cristobal](https://community.mrtrix.org/u/Cristobal)\ **Replies:** 0\ **Last updated:** [June 30, 2025, 3:25pm UTC](https://community.mrtrix.org/t/clarification-on-tckmap-tdi-contrast-behavior/8430 "2025-06-30T15:25:28Z")
Dear MRtrix experts, I have a question regarding the tckmap command using the TDI contrast. One aspect that is not entirely clear to me is how streamline points are counted within each voxel. Specifically, if a single … --- ## [Dilating of brain mask and some other general queries](https://community.mrtrix.org/t/dilating-of-brain-mask-and-some-other-general-queries/1304)
**Author:** [@Michiko](https://community.mrtrix.org/u/Michiko)\ **Replies:** 15\ **Last updated:** [June 19, 2025, 8:05am UTC](https://community.mrtrix.org/t/dilating-of-brain-mask-and-some-other-general-queries/1304 "2025-06-19T08:05:51Z")
Dear MRtrix Community, I was wondering if it is always necessary to perform mask dilation as mentioned/advised in a couple of posts (e.g. Beginner: Connectome pipeline). I previously followed the HCP tutorial which simp… --- ## [Which FOD file to use for TractSeg in subject space](https://community.mrtrix.org/t/which-fod-file-to-use-for-tractseg-in-subject-space/8407)
**Author:** [@Tanja](https://community.mrtrix.org/u/Tanja)\ **Replies:** 1\ **Last updated:** [June 16, 2025, 3:01pm UTC](https://community.mrtrix.org/t/which-fod-file-to-use-for-tractseg-in-subject-space/8407 "2025-06-16T15:01:52Z")
Hi everyone, I have been trying to extract average tract-wise FD, FC, and FDC and so far I’ve been running TractSeg on the template FOD since the FD/FC/FDC maps are in template space too and the tract masks can be appli… --- ## [How to incorporate ACT framework when including small brainstem substructures?](https://community.mrtrix.org/t/how-to-incorporate-act-framework-when-including-small-brainstem-substructures/8387)
**Author:** [@monicaiduran](https://community.mrtrix.org/u/monicaiduran)\ **Replies:** 1\ **Last updated:** [June 12, 2025, 11:48pm UTC](https://community.mrtrix.org/t/how-to-incorporate-act-framework-when-including-small-brainstem-substructures/8387 "2025-06-12T23:48:17Z")
Hi MRtrix team, I’m working on a connectomics pipeline that includes small brainstem substructures (e.g., reticular nuclei, arousal-related nodes), and I’m wondering whether there is a feasible way to incorporate the AC… --- ## [Clarification on -seed\_dynamic: Is a WM mask required when not using ACT?](https://community.mrtrix.org/t/clarification-on-seed-dynamic-is-a-wm-mask-required-when-not-using-act/8386)
**Author:** [@monicaiduran](https://community.mrtrix.org/u/monicaiduran)\ **Replies:** 0\ **Last updated:** [June 4, 2025, 4:48pm UTC](https://community.mrtrix.org/t/clarification-on-seed-dynamic-is-a-wm-mask-required-when-not-using-act/8386 "2025-06-04T16:48:20Z")
Hi MRtrix team, I’m using the -seed\_dynamic option in tckgen to generate whole-brain tractograms and had a few questions about best practices when not using ACT. In our study, we are specifically including small brainst… --- ## [Tckresample -step showing inhomogenous steps](https://community.mrtrix.org/t/tckresample-step-showing-inhomogenous-steps/8379)
**Author:** [@lconcha](https://community.mrtrix.org/u/lconcha)\ **Replies:** 0\ **Last updated:** [May 30, 2025, 7:47pm UTC](https://community.mrtrix.org/t/tckresample-step-showing-inhomogenous-steps/8379 "2025-05-30T19:47:18Z")
Hello. When using tckresample -step \, I get streamlines with (nearly) homogeneous step sizes, except for the step between the first and second points. This is noticeable in the figure below. A single streamline… --- ## [Tckstats with and without SIFT2 : no streamline count change?](https://community.mrtrix.org/t/tckstats-with-and-without-sift2-no-streamline-count-change/8377)
**Author:** [@A.Rossez](https://community.mrtrix.org/u/A.Rossez)\ **Replies:** 1\ **Last updated:** [May 28, 2025, 3:00pm UTC](https://community.mrtrix.org/t/tckstats-with-and-without-sift2-no-streamline-count-change/8377 "2025-05-28T15:00:38Z")
Hello dear MRtrix community ! :wave: :grinning: I’ve been starting to use SIFT following this paragraph from MRtrix : Use of SIFT for quantifying pathways of interest In some circumstances, researchers may be interest… --- ## [Mrview is slow to respond even load 5 million streamlines](https://community.mrtrix.org/t/mrview-is-slow-to-respond-even-load-5-million-streamlines/8292)
**Author:** [@Yufeng\_He](https://community.mrtrix.org/u/Yufeng_He)\ **Replies:** 2\ **Last updated:** [March 24, 2025, 7:53am UTC](https://community.mrtrix.org/t/mrview-is-slow-to-respond-even-load-5-million-streamlines/8292 "2025-03-24T07:53:42Z")
Dear experts, When I’m using mrview to browse my tck file, mrview becomes very laggy, even though my tck file only has 50,000 streamlines. My laptop’s chip is M4pro, running memory is 24G. I would like to know if this … --- ## [What the result of two shells (one 0, one 1500) using msmt\_csd should look like?](https://community.mrtrix.org/t/what-the-result-of-two-shells-one-0-one-1500-using-msmt-csd-should-look-like/8291)
**Author:** [@Yufeng\_He](https://community.mrtrix.org/u/Yufeng_He)\ **Replies:** 2\ **Last updated:** [March 22, 2025, 11:27am UTC](https://community.mrtrix.org/t/what-the-result-of-two-shells-one-0-one-1500-using-msmt-csd-should-look-like/8291 "2025-03-22T11:27:20Z")
Dear Community, I’m generating FOD for my two shells(0,1500), 60 directions data, using the MSMT-CSD method.I want to check my generated fod map to make sure everything is ok. But I suddenly realised that there are very… [Next page](https://community.mrtrix.org/tag/tractography/14.md?match_all_tags=true&page=1&tags%5B%5D=tractography)