# \#diffusion

**URL:** https://discourse.slicer.org/tag/diffusion/11.md

[Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md)

---

## [Workflow Questions on SWM Analysis with UKFtractography and whitematteranalysis](https://discourse.slicer.org/t/workflow-questions-on-swm-analysis-with-ukftractography-and-whitematteranalysis/44753)

<div class="topic-metadata">

**Author:** [@younghoo](https://discourse.slicer.org/u/younghoo)\
**Replies:** 12\
**Last updated:** [January 18, 2026, 3:50am UTC](https://discourse.slicer.org/t/workflow-questions-on-swm-analysis-with-ukftractography-and-whitematteranalysis/44753 "2026-01-18T03:50:11Z")

</div>

Dear Experts, I am attempting to replicate the methodology described in the following paper and have a few questions that I hope you can help clarify: Wang, S., Zhang, F., Zeng, Q., Hong, H., Zhang, Y., Xie, L., Lin, M…

---

## [Using Slicer for Diffusion MRI in cancer research? We want to hear from you!](https://discourse.slicer.org/t/using-slicer-for-diffusion-mri-in-cancer-research-we-want-to-hear-from-you/42986)

<div class="topic-metadata">

**Author:** [@ljod](https://discourse.slicer.org/u/ljod)\
**Replies:** 1\
**Last updated:** [May 21, 2025, 3:03pm UTC](https://discourse.slicer.org/t/using-slicer-for-diffusion-mri-in-cancer-research-we-want-to-hear-from-you/42986 "2025-05-21T15:03:22Z")

</div>

Are you using Slicer for diffusion MRI in cancer research? We’d love to hear how you’re using it and get your quick feedback! Please respond by Monday May 19 (or Tuesday at the latest) to help our funding efforts to impr…

---

## [Flipped NIFTI image compared to original Nrrd File](https://discourse.slicer.org/t/flipped-nifti-image-compared-to-original-nrrd-file/479)

<div class="topic-metadata">

**Author:** [@belleauel](https://discourse.slicer.org/u/belleauel)\
**Replies:** 12\
**Last updated:** [August 12, 2024, 8:56pm UTC](https://discourse.slicer.org/t/flipped-nifti-image-compared-to-original-nrrd-file/479 "2024-08-12T20:56:58Z")

</div>

Operating system: Slicer version: Expected behavior: Actual behavior: Hello Slicer Experts, I had done some initial processing of my DTI data in Slicer. Now, I have converted the files to nifti via DWIConvert so t…

---

## [ALPS index calculation- DTI sequence](https://discourse.slicer.org/t/alps-index-calculation-dti-sequence/28721)

<div class="topic-metadata">

**Author:** [@emin](https://discourse.slicer.org/u/emin)\
**Replies:** 2\
**Last updated:** [April 16, 2024, 7:08am UTC](https://discourse.slicer.org/t/alps-index-calculation-dti-sequence/28721 "2024-04-16T07:08:59Z")

</div>

hi, i need the calculate ALPS index for DTI sequence, anyone can describe steps? help me

---

## [calculate the ADC map from DWI data](https://discourse.slicer.org/t/calculate-the-adc-map-from-dwi-data/33519)

<div class="topic-metadata">

**Author:** [@smati\_wissem](https://discourse.slicer.org/u/smati_wissem)\
**Replies:** 0\
**Last updated:** [December 26, 2023, 12:02am UTC](https://discourse.slicer.org/t/calculate-the-adc-map-from-dwi-data/33519 "2023-12-26T00:02:41Z")

</div>

Hello everyone, it’s been 5 days that I’ve been searching for a solution to my problem, but I haven’t found one. So, I’m reaching out for your help. My question is how to calculate the ADC volume from a DWI volume. Than…

---

## [Run a loadable module from python console](https://discourse.slicer.org/t/run-a-loadable-module-from-python-console/3427)

<div class="topic-metadata">

**Author:** [@Sanjeev\_Grampurohit](https://discourse.slicer.org/u/Sanjeev_Grampurohit)\
**Replies:** 5\
**Last updated:** [August 15, 2023, 3:26am UTC](https://discourse.slicer.org/t/run-a-loadable-module-from-python-console/3427 "2023-08-15T03:26:22Z")

</div>

I want to be able to run the tractographyinteractiveseeding module from the python console. It is a loadable module which I think is why slicer.cli.run(, ) doesn’t seem to work. How do I run this module? Also, given a mo…

---

## [Adding an icon to identify an extension](https://discourse.slicer.org/t/adding-an-icon-to-identify-an-extension/30562)

<div class="topic-metadata">

**Author:** [@jhlegarreta](https://discourse.slicer.org/u/jhlegarreta)\
**Replies:** 11\
**Last updated:** [July 25, 2023, 4:03pm UTC](https://discourse.slicer.org/t/adding-an-icon-to-identify-an-extension/30562 "2023-07-25T16:03:08Z")

</div>

Hi, when having adding some of the diffusion-related extension to the favorites toolbar I see that all have the same default icon used for extensions, which makes it difficult to recognize them. What is the appropri…

---

## [tractography single color tract not multi-color tract](https://discourse.slicer.org/t/tractography-single-color-tract-not-multi-color-tract/29952)

<div class="topic-metadata">

**Author:** [@GunnarE](https://discourse.slicer.org/u/GunnarE)\
**Replies:** 2\
**Last updated:** [July 24, 2023, 10:43pm UTC](https://discourse.slicer.org/t/tractography-single-color-tract-not-multi-color-tract/29952 "2023-07-24T22:43:20Z")

</div>

Hi Slicer community, We have been following multiple tutorials from Dr. Sonia Pujol on diffusion tractography including “Exploring Peritumoral White Matter Fibers for Neurosurgical Planning”, “Diffusion MRI Analsyis”, a…

---

## [Displaying a colorbar across viewers for diffusion scalar maps on tractography data](https://discourse.slicer.org/t/displaying-a-colorbar-across-viewers-for-diffusion-scalar-maps-on-tractography-data/30564)

<div class="topic-metadata">

**Author:** [@jhlegarreta](https://discourse.slicer.org/u/jhlegarreta)\
**Replies:** 7\
**Last updated:** [July 24, 2023, 5:42pm UTC](https://discourse.slicer.org/t/displaying-a-colorbar-across-viewers-for-diffusion-scalar-maps-on-tractography-data/30564 "2023-07-24T17:42:36Z")

</div>

Hi, is it possible to add a colorbar across the Slicer viewers (just as shown in the image in this post for another type of data) when we load some tractography data and load an associated scalar map, e.g. FA? If yes, h…

---

## [Fail to launch FiberTractMeasurements CLI module on Windows](https://discourse.slicer.org/t/fail-to-launch-fibertractmeasurements-cli-module-on-windows/30708)

<div class="topic-metadata">

**Author:** [@Kening\_Zhang](https://discourse.slicer.org/u/Kening_Zhang)\
**Replies:** 3\
**Last updated:** [July 21, 2023, 2:58pm UTC](https://discourse.slicer.org/t/fail-to-launch-fibertractmeasurements-cli-module-on-windows/30708 "2023-07-21T14:58:30Z")

</div>

Dear developers, When I type this command to use cli FiberTractMeasurements on my windows computer, some errors jumped, which says, can’t find xxx.dll, and cannot run the code, reinstalling the program may resolve …

---

## [Slicer FiberTractMeasurements unable to find libSlicerBaseLogic](https://discourse.slicer.org/t/slicer-fibertractmeasurements-unable-to-find-libslicerbaselogic/30357)

<div class="topic-metadata">

**Author:** [@jhlegarreta](https://discourse.slicer.org/u/jhlegarreta)\
**Replies:** 11\
**Last updated:** [July 6, 2023, 2:35pm UTC](https://discourse.slicer.org/t/slicer-fibertractmeasurements-unable-to-find-libslicerbaselogic/30357 "2023-07-06T14:35:33Z")

</div>

Hi, I am trying to run WMA on a given dataset. The process runs fine until the moment where the FiberTractMeasurements module in Slicer is called. The tool writes the following to the std output: \<wm\_apply\_ORG\_atlas\_to…

---

## [Intensity normalization](https://discourse.slicer.org/t/intensity-normalization/28024)

<div class="topic-metadata">

**Author:** [@Floren](https://discourse.slicer.org/u/Floren)\
**Replies:** 1\
**Last updated:** [March 2, 2023, 6:24am UTC](https://discourse.slicer.org/t/intensity-normalization/28024 "2023-03-02T06:24:48Z")

</div>

Hello, everyone! I am working with prostate adc maps and trying to measure adc value for prostate tumors in order to demonstrate that there is a correlation between adc value and Gleason score. I understood that i must…

---

## [Change b value on ADC](https://discourse.slicer.org/t/change-b-value-on-adc/27777)

<div class="topic-metadata">

**Author:** [@Floren](https://discourse.slicer.org/u/Floren)\
**Replies:** 0\
**Last updated:** [February 12, 2023, 11:15am UTC](https://discourse.slicer.org/t/change-b-value-on-adc/27777 "2023-02-12T11:15:36Z")

</div>

Is it posible to change the b value on the ADC maps using 3d slicer?

---

## [Diffusion brain masking](https://discourse.slicer.org/t/diffusion-brain-masking/7811)

<div class="topic-metadata">

**Author:** [@Lungimiro](https://discourse.slicer.org/u/Lungimiro)\
**Replies:** 21\
**Last updated:** [January 16, 2023, 8:29am UTC](https://discourse.slicer.org/t/diffusion-brain-masking/7811 "2023-01-16T08:29:58Z")

</div>

Operating system: MacOS Mojave 10.14 Slicer version: 4.10.2 MR: Philips Hello!! I wanna create a diffusion brain mask but I have the following problem: "Diffusion Brain Masking standard error: ERROR: In /Volumes/Da…

---

## [What's wrong with my DWI? Failed to convert from DWI to tensors](https://discourse.slicer.org/t/whats-wrong-with-my-dwi-failed-to-convert-from-dwi-to-tensors/26864)

<div class="topic-metadata">

**Author:** [@peter\_adidharma](https://discourse.slicer.org/u/peter_adidharma)\
**Replies:** 3\
**Last updated:** [December 22, 2022, 1:40pm UTC](https://discourse.slicer.org/t/whats-wrong-with-my-dwi-failed-to-convert-from-dwi-to-tensors/26864 "2022-12-22T13:40:38Z")

</div>

Hi all, I’ve been working to do some tractography using slicerDMRI, but seems to encounter the same problem with all DWI files that i have as i failed to convert it to tensors. Here, I attached the .nrrd file of our DWI…

---

## [Export DTI as Ply rotational error](https://discourse.slicer.org/t/export-dti-as-ply-rotational-error/26478)

<div class="topic-metadata">

**Author:** [@yuanci](https://discourse.slicer.org/u/yuanci)\
**Replies:** 7\
**Last updated:** [December 11, 2022, 4:38am UTC](https://discourse.slicer.org/t/export-dti-as-ply-rotational-error/26478 "2022-12-11T04:38:16Z")

</div>

Hi, I’m still trying to figure out the full capabilities of Slicer, and just recently started using the DMRI extension. I tried to export a tract as PLY using the “Export tractography to PLY (mesh)” tool but every time …

---

## [Load DSI Studio (\*.trk.gz) or TrackVis (\*.trk) tracks in Slicer](https://discourse.slicer.org/t/load-dsi-studio-trk-gz-or-trackvis-trk-tracks-in-slicer/1356)

<div class="topic-metadata">

**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 16\
**Last updated:** [July 28, 2022, 11:05am UTC](https://discourse.slicer.org/t/load-dsi-studio-trk-gz-or-trackvis-trk-tracks-in-slicer/1356 "2022-07-28T11:05:13Z")

</div>

Does anyone have experience converting and then loading fibertrack generated by these software into 3D Slicer ? Is there any recommended pathway to export tracts and import them into Slicer ? We are thinking of these …

---

## [Tractography issue](https://discourse.slicer.org/t/tractography-issue/24093)

<div class="topic-metadata">

**Author:** [@massimo](https://discourse.slicer.org/u/massimo)\
**Replies:** 4\
**Last updated:** [June 30, 2022, 6:21pm UTC](https://discourse.slicer.org/t/tractography-issue/24093 "2022-06-30T18:21:55Z")

</div>

Operating system: Mac OSX Monterey Slicer version:5.0.2 Expected behavior: Tractography visualization Actual behavior: Errors in data import Dear Community, I’m trying to create a 3d model of a tractography to view …

---

## [Problem with myvmtkmeshDlabeling](https://discourse.slicer.org/t/problem-with-myvmtkmeshdlabeling/22953)

<div class="topic-metadata">

**Author:** [@19lollo95](https://discourse.slicer.org/u/19lollo95)\
**Replies:** 0\
**Last updated:** [April 13, 2022, 10:09pm UTC](https://discourse.slicer.org/t/problem-with-myvmtkmeshdlabeling/22953 "2022-04-13T22:09:08Z")

</div>

I’m working with macOS operating system on mac with M1 processor. I’m having problems in order to obtain a meshDxx.vtu (starting from 2 files meshR.vtu and Dxx.mhd) which associates the values of the tensor built in Dxx…

---

## [FA measurement using data probe or any other method](https://discourse.slicer.org/t/fa-measurement-using-data-probe-or-any-other-method/9654)

<div class="topic-metadata">

**Author:** [@HariES](https://discourse.slicer.org/u/HariES)\
**Replies:** 7\
**Last updated:** [March 26, 2022, 5:01pm UTC](https://discourse.slicer.org/t/fa-measurement-using-data-probe-or-any-other-method/9654 "2022-03-26T17:01:27Z")

</div>

How to measure fractional anisotropy in roi after creating scalar maps.

---

## [Diffusion module in 4.13 version cannot complete the reconstruction of fiber bundle](https://discourse.slicer.org/t/diffusion-module-in-4-13-version-cannot-complete-the-reconstruction-of-fiber-bundle/19896)

<div class="topic-metadata">

**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 10\
**Last updated:** [March 13, 2022, 4:29pm UTC](https://discourse.slicer.org/t/diffusion-module-in-4-13-version-cannot-complete-the-reconstruction-of-fiber-bundle/19896 "2022-03-13T16:29:56Z")

</div>

Win10 64 I don’t know if this is a mistake My friend and I have tried multiple versions of 4.13 Slicer But in the last step, when setting the seed to display the fiber bundle, it can’t be displayed. The same data, th…

---

## [DWI ADC calculation](https://discourse.slicer.org/t/dwi-adc-calculation/17641)

<div class="topic-metadata">

**Author:** [@RO786](https://discourse.slicer.org/u/RO786)\
**Replies:** 11\
**Last updated:** [March 11, 2022, 11:44am UTC](https://discourse.slicer.org/t/dwi-adc-calculation/17641 "2022-03-11T11:44:14Z")

</div>

Operating system:Windows 10 Slicer version: 4.11.2020 Hello everyone, I’m quite new to the 3D slicer platform so very much appreciate any advice. This is not my field of expertise. I want to measure the ADC of the ex…

---

## [FSL transfer to nrrd have no output file](https://discourse.slicer.org/t/fsl-transfer-to-nrrd-have-no-output-file/22412)

<div class="topic-metadata">

**Author:** [@talelee](https://discourse.slicer.org/u/talelee)\
**Replies:** 0\
**Last updated:** [March 9, 2022, 2:51pm UTC](https://discourse.slicer.org/t/fsl-transfer-to-nrrd-have-no-output-file/22412 "2022-03-09T14:51:01Z")

</div>

The only hint in my dialog box Diffusion-weighted DICOM Import (DWIConvert) standard output: ======= DWI Convert Tool Program========= INPUT VOLUME: /home/lee/100417/data/data.nii.gz

---

## [Error with DiffusionQC module (GradQC)](https://discourse.slicer.org/t/error-with-diffusionqc-module-gradqc/17330)

<div class="topic-metadata">

**Author:** [@amvoid](https://discourse.slicer.org/u/amvoid)\
**Replies:** 4\
**Last updated:** [May 1, 2021, 2:23pm UTC](https://discourse.slicer.org/t/error-with-diffusionqc-module-gradqc/17330 "2021-05-01T14:23:55Z")

</div>

Operating system: win10/Ubuntu 20 Slicer version: 4.11 After I install DiffusionQC extension, there come out an error whenever I star Slicer. I notice that GradQC failed to install, but I don’t know why. Traceback (mo…

---

## [Trying to create custom DTI volume](https://discourse.slicer.org/t/trying-to-create-custom-dti-volume/17318)

<div class="topic-metadata">

**Author:** [@haz\_lanz](https://discourse.slicer.org/u/haz_lanz)\
**Replies:** 3\
**Last updated:** [April 26, 2021, 11:26pm UTC](https://discourse.slicer.org/t/trying-to-create-custom-dti-volume/17318 "2021-04-26T23:26:51Z")

</div>

Hello, I am trying to use the diffusion tractography capabilities of 3DSlicer to visualise some data I have collected from my PhD research. It is similar to diffusion weighted MRI but does not produce diffusion weighted…

---

## [ADC values on a DWI scan](https://discourse.slicer.org/t/adc-values-on-a-dwi-scan/1352)

<div class="topic-metadata">

**Author:** [@faraz1368](https://discourse.slicer.org/u/faraz1368)\
**Replies:** 11\
**Last updated:** [April 23, 2021, 9:09pm UTC](https://discourse.slicer.org/t/adc-values-on-a-dwi-scan/1352 "2021-04-23T21:09:35Z")

</div>

Hi, I wanted to know if it is possible to load a DWI scan into slicer, draw a ROI and find the ADC values (in 10-6 mm2/s) (average and a distribution curve) corresponding to that ROI. Thank you for your responses Fara…

---

## [How to calculate the average length and FA value of fiber bundles](https://discourse.slicer.org/t/how-to-calculate-the-average-length-and-fa-value-of-fiber-bundles/16225)

<div class="topic-metadata">

**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 0\
**Last updated:** [February 26, 2021, 1:26am UTC](https://discourse.slicer.org/t/how-to-calculate-the-average-length-and-fa-value-of-fiber-bundles/16225 "2021-02-26T01:26:15Z")

</div>

How to calculate the average length and FA value of fiber bundles like this picture?For example, if I set a label or model and get the corresponding fiber bundle, how to calculate the average length and FA value of the f…

---

## [DWI to DTI Estimation Problem](https://discourse.slicer.org/t/dwi-to-dti-estimation-problem/719)

<div class="topic-metadata">

**Author:** [@AsliBeriL](https://discourse.slicer.org/u/AsliBeriL)\
**Replies:** 19\
**Last updated:** [August 21, 2020, 6:12pm UTC](https://discourse.slicer.org/t/dwi-to-dti-estimation-problem/719 "2020-08-21T18:12:21Z")

</div>

Operating system: Win 10 Pro Slicer version: 4.5.0-1 Hello everyone, I want DWI images convert to DTI and tractography. First step, i created .nrrd file, baseline and mask. Later, DWI to DTI estimation module is worki…

---

## [Ukf tractography](https://discourse.slicer.org/t/ukf-tractography/2747)

<div class="topic-metadata">

**Author:** [@Jin](https://discourse.slicer.org/u/Jin)\
**Replies:** 7\
**Last updated:** [July 28, 2020, 1:19pm UTC](https://discourse.slicer.org/t/ukf-tractography/2747 "2020-07-28T13:19:00Z")

</div>

Operating system:windows 10 Slicer version:4.8.0 Expected behavior: DTI Process Actual behavior: Standard error The current UKF Tractography is different from the tutorial(4.4)

---

## [Signal loss after epi correction](https://discourse.slicer.org/t/signal-loss-after-epi-correction/12723)

<div class="topic-metadata">

**Author:** [@mali](https://discourse.slicer.org/u/mali)\
**Replies:** 5\
**Last updated:** [July 25, 2020, 8:06pm UTC](https://discourse.slicer.org/t/signal-loss-after-epi-correction/12723 "2020-07-25T20:06:07Z")

</div>

Dear Slicer community, I hope you can help me with an issue I am struggling with. Iam currently working on DTI scans using Slicer and the PNL Pipeline. After applying epi correction (epi.sh) I am getting images that loo…

[Next page](https://discourse.slicer.org/tag/diffusion/11.md?match_all_tags=true&page=1&tags%5B%5D=diffusion)