# SlicerDMRI **URL:** https://discourse.slicer.org/c/community/slicerdmri/16.md?page=1 [Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md) **Page:** 2 --- ## [Fibre length measurements](https://discourse.slicer.org/t/fibre-length-measurements/23676)
**Author:** [@njeffery](https://discourse.slicer.org/u/njeffery)\ **Replies:** 1\ **Last updated:** [June 1, 2022, 7:03pm UTC](https://discourse.slicer.org/t/fibre-length-measurements/23676 "2022-06-01T19:03:42Z")
Hi 3Dslicer community Hoping someone has a solution out there. I have a vtk file with about 300 fibres in it. I need the length of each fibre. Seems a trivial task but I cannot find a solution. Diffusion\>quantify\>tr… --- ## [Help loading DICOM](https://discourse.slicer.org/t/help-loading-dicom/13930)
**Author:** [@Felipe\_Suntaxi](https://discourse.slicer.org/u/Felipe_Suntaxi)\ **Replies:** 2\ **Last updated:** [June 1, 2022, 8:51am UTC](https://discourse.slicer.org/t/help-loading-dicom/13930 "2022-06-01T08:51:30Z")
Hello. I’m new to the Slicer DMRI. I’m trying to load some dicom data but I get this error. Diffusion-weighted DICOM Import (DWIConvert) standard error: Exception thrown while reading DICOM volume itk::InvalidRequeste… --- ## [DTI Statistics for a specific ROI of a fiber?](https://discourse.slicer.org/t/dti-statistics-for-a-specific-roi-of-a-fiber/10385)
**Author:** [@LearningSlicerYay](https://discourse.slicer.org/u/LearningSlicerYay)\ **Replies:** 4\ **Last updated:** [March 28, 2022, 8:35am UTC](https://discourse.slicer.org/t/dti-statistics-for-a-specific-roi-of-a-fiber/10385 "2022-03-28T08:35:47Z")
Hi all, I generated my fiber tracts using interactive markup. I would like to generate statistics based on a specific region of these tracts. Is there a way I can do this? Many thanks, --- ## [FA measurement using data probe or any other method](https://discourse.slicer.org/t/fa-measurement-using-data-probe-or-any-other-method/9654)
**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")
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)
**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")
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… --- ## [Siemens mosaic to DICOM stock](https://discourse.slicer.org/t/siemens-mosaic-to-dicom-stock/21041)
**Author:** [@Pawel\_Ozga](https://discourse.slicer.org/u/Pawel_Ozga)\ **Replies:** 2\ **Last updated:** [December 14, 2021, 8:55am UTC](https://discourse.slicer.org/t/siemens-mosaic-to-dicom-stock/21041 "2021-12-14T08:55:54Z")
Hi, I’m sorry if I’m writing this question in the wrong place but I don’t know where to ask. I have an exam made on siemens MR and the DTI sequence is stored as a mosaic. Is there any way to convert the exam so that DT… --- ## [SlicerDMRI Tractography Display, Fiber bundle selection with custom function](https://discourse.slicer.org/t/slicerdmri-tractography-display-fiber-bundle-selection-with-custom-function/17566)
**Author:** [@simonoxen](https://discourse.slicer.org/u/simonoxen)\ **Replies:** 2\ **Last updated:** [May 19, 2021, 4:27pm UTC](https://discourse.slicer.org/t/slicerdmri-tractography-display-fiber-bundle-selection-with-custom-function/17566 "2021-05-19T16:27:57Z")
Hi, would it be possible to set up different ways of fiber bundle selection other than ROI? I would be interested in using a sphere for example, simulating a simple volume of tissue activated and displaying overlapping … --- ## [How to run cast scalar volume module from command line](https://discourse.slicer.org/t/how-to-run-cast-scalar-volume-module-from-command-line/17595)
**Author:** [@shael](https://discourse.slicer.org/u/shael)\ **Replies:** 2\ **Last updated:** [May 14, 2021, 6:53pm UTC](https://discourse.slicer.org/t/how-to-run-cast-scalar-volume-module-from-command-line/17595 "2021-05-14T18:53:21Z")
Hi community, I’m trying to run the Cast Scalar Volume module from the command line to convert a nifti brain mask into a uchar nrrd file format. I can successfully run the command from the Slicer GUI, and when I click o… --- ## [cannot open .nhdr file on Slicer](https://discourse.slicer.org/t/cannot-open-nhdr-file-on-slicer/16579)
**Author:** [@Tamires\_Zanao](https://discourse.slicer.org/u/Tamires_Zanao)\ **Replies:** 1\ **Last updated:** [April 14, 2021, 6:16am UTC](https://discourse.slicer.org/t/cannot-open-nhdr-file-on-slicer/16579 "2021-04-14T06:16:32Z")
Hi everyone! I am trying to proceed with dwi QC, but I cannot open my axis aligned .nhdr dwi image on Slicer. I checked with unu head and the information of the image itself looks fine. I can also open/visualize my previ… --- ## [DTIPrep installation](https://discourse.slicer.org/t/dtiprep-installation/1885)
**Author:** [@nahid](https://discourse.slicer.org/u/nahid)\ **Replies:** 2\ **Last updated:** [March 16, 2021, 5:24pm UTC](https://discourse.slicer.org/t/dtiprep-installation/1885 "2021-03-16T17:24:08Z")
Dear 3D Slicer experts I am pretty new in 3d Slicer. I want to use DTIPrep but it is not in the list of extensions to be installed. I have downloaded it separately but I don’t know how to install it. Any help appreciat… --- ## [SlicerDMRI tractography measurements](https://discourse.slicer.org/t/slicerdmri-tractography-measurements/16468)
**Author:** [@amymanson](https://discourse.slicer.org/u/amymanson)\ **Replies:** 2\ **Last updated:** [March 11, 2021, 10:42am UTC](https://discourse.slicer.org/t/slicerdmri-tractography-measurements/16468 "2021-03-11T10:42:54Z")
Hi, I was wondering if anyone could clarify the meaning of one of the measurement results produced when running Diffusion-\>Quantify-\>Tractography Measurements on DTI data? The measurements produced are (among others) Nu… --- ## [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)
**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")
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… --- ## [dMRI Extension Files -- Where do they end up?](https://discourse.slicer.org/t/dmri-extension-files-where-do-they-end-up/14246)
**Author:** [@mgc26](https://discourse.slicer.org/u/mgc26)\ **Replies:** 6\ **Last updated:** [November 4, 2020, 2:00am UTC](https://discourse.slicer.org/t/dmri-extension-files-where-do-they-end-up/14246 "2020-11-04T02:00:15Z")
I’ve been trying to complete the whitematteranalysis, but stuck on the last step as I cannot locate the SlicerDMRI extension files on my Ubuntu box. The step I’m stuck on: 8. Fiber tract diffusion measurements wm\_diff… --- ## [Trying to do tractography from DICOM DTI](https://discourse.slicer.org/t/trying-to-do-tractography-from-dicom-dti/13964)
**Author:** [@Cerebellum](https://discourse.slicer.org/u/Cerebellum)\ **Replies:** 1\ **Last updated:** [October 9, 2020, 8:22pm UTC](https://discourse.slicer.org/t/trying-to-do-tractography-from-dicom-dti/13964 "2020-10-09T20:22:29Z")
Hello! Recently I found an old disk from the place I used to work with where I saved my own brain MRI (I used to do tractography with FiberTrak in a Philips station for neuroanatomy teaching purposes). In that disk I ha… --- ## [No b0! Error with the brain masking process](https://discourse.slicer.org/t/no-b0-error-with-the-brain-masking-process/13448)
**Author:** [@Nicholas.jacobson](https://discourse.slicer.org/u/Nicholas.jacobson)\ **Replies:** 3\ **Last updated:** [September 14, 2020, 3:57pm UTC](https://discourse.slicer.org/t/no-b0-error-with-the-brain-masking-process/13448 "2020-09-14T15:57:51Z")
Hello, We are starting to research Tractragraphy for 3d printing purposes and struggling to get the process started with our images. We have loaded all of our dwi images but run into a problem with the brain masking pro… --- ## [Converting multi channel mask or colored mask to colored DICO Mask](https://discourse.slicer.org/t/converting-multi-channel-mask-or-colored-mask-to-colored-dico-mask/12952)
**Author:** [@Nawaf\_Khan](https://discourse.slicer.org/u/Nawaf_Khan)\ **Replies:** 0\ **Last updated:** [August 11, 2020, 10:22pm UTC](https://discourse.slicer.org/t/converting-multi-channel-mask-or-colored-mask-to-colored-dico-mask/12952 "2020-08-11T22:22:28Z")
I have question I Have DATA which I segmented on the slicer and its segmentation mask color is pink yellow and green I want to export all these segmentation masks with these color as Dicom any idea will be helpful thanks … --- ## [Signal loss after epi correction](https://discourse.slicer.org/t/signal-loss-after-epi-correction/12723)
**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")
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… --- ## [dMRI Scalar Maps & Meausrements](https://discourse.slicer.org/t/dmri-scalar-maps-meausrements/11933)
**Author:** [@LearningSlicerYay](https://discourse.slicer.org/u/LearningSlicerYay)\ **Replies:** 4\ **Last updated:** [June 9, 2020, 4:53pm UTC](https://discourse.slicer.org/t/dmri-scalar-maps-meausrements/11933 "2020-06-09T16:53:26Z")
Hi everyone, I could not find this info when going through the documentation, but I was wondering if there were definitions or more info about how the following are calculated using dMRI: -Relative Anisotropy -Determi… --- ## [Bulk scalars / statistics](https://discourse.slicer.org/t/bulk-scalars-statistics/11255)
**Author:** [@LearningSlicerYay](https://discourse.slicer.org/u/LearningSlicerYay)\ **Replies:** 2\ **Last updated:** [April 30, 2020, 5:35pm UTC](https://discourse.slicer.org/t/bulk-scalars-statistics/11255 "2020-04-30T17:35:45Z")
Hi everyone, I have processed my DTI and am interested in getting statistics on certain areas I made labels for. Right now I am creating each map using the “Diffusion Tensor Scalar Maps” module, and then using the Label… --- ## [Fibers are not well achieve in 3D Slicer but can be displayed in DTI Studio](https://discourse.slicer.org/t/fibers-are-not-well-achieve-in-3d-slicer-but-can-be-displayed-in-dti-studio/11103)
**Author:** [@researchtomliu](https://discourse.slicer.org/u/researchtomliu)\ **Replies:** 2\ **Last updated:** [April 14, 2020, 4:27pm UTC](https://discourse.slicer.org/t/fibers-are-not-well-achieve-in-3d-slicer-but-can-be-displayed-in-dti-studio/11103 "2020-04-14T16:27:56Z")
Dear friends, when I deal with DTI data, I found that the results of 3D slicer were different from using DTI studio. The fibers such as of internal capsule were short and fragmented in 3D slicer and they were complete in… --- ## [Assessing average displacement resulting from a linear transform](https://discourse.slicer.org/t/assessing-average-displacement-resulting-from-a-linear-transform/9318)
**Author:** [@DTI](https://discourse.slicer.org/u/DTI)\ **Replies:** 7\ **Last updated:** [April 1, 2020, 1:01pm UTC](https://discourse.slicer.org/t/assessing-average-displacement-resulting-from-a-linear-transform/9318 "2020-04-01T13:01:17Z")
Hi, Is there a way in Slicer to calculate the mean DTI distortion (e.g. as mean transform needed to align DTI to T2w, like the root mean square deviation). I found this: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC51… --- ## [Problems with fibers' directions](https://discourse.slicer.org/t/problems-with-fibers-directions/10759)
**Author:** [@doc-xie](https://discourse.slicer.org/u/doc-xie)\ **Replies:** 2\ **Last updated:** [March 25, 2020, 9:00am UTC](https://discourse.slicer.org/t/problems-with-fibers-directions/10759 "2020-03-25T09:00:48Z")
Version: 4.11.0-2020-02-26 System: Mac MR scanner: GE, 3.0T Problem: The components of the diffusion data can be checked successfully in Volume module and the FA map can be derived with Diffusion Tensor Estimation. T… --- ## [DWI data denoising](https://discourse.slicer.org/t/dwi-data-denoising/10743)
**Author:** [@Adam1122](https://discourse.slicer.org/u/Adam1122)\ **Replies:** 3\ **Last updated:** [March 21, 2020, 1:54pm UTC](https://discourse.slicer.org/t/dwi-data-denoising/10743 "2020-03-21T13:54:05Z")
Hello all, does the current Slicer version enable to apply denoising on the DWI data? I haven´t found any DWI denoising filter. In Slicer 3.6 there were implemented 3 DWI filters ( Joint Rician, Rician and Unbiased NLM).… --- ## [A few questions](https://discourse.slicer.org/t/a-few-questions/10563)
**Author:** [@LearningSlicerYay](https://discourse.slicer.org/u/LearningSlicerYay)\ **Replies:** 4\ **Last updated:** [March 6, 2020, 2:32pm UTC](https://discourse.slicer.org/t/a-few-questions/10563 "2020-03-06T14:32:58Z")
Hi all, Working with Slicer 4.10.1 and have a few questions: Is there a way to adjust for eddy current in this (or 4.10.2) version? I have read the FAQ but cannot find the “GTRACT” extension that they mention. Wha… --- ## [T1 and DWI co-registration - is it automatic](https://discourse.slicer.org/t/t1-and-dwi-co-registration-is-it-automatic/9272)
**Author:** [@LearningSlicerYay](https://discourse.slicer.org/u/LearningSlicerYay)\ **Replies:** 6\ **Last updated:** [February 25, 2020, 10:10pm UTC](https://discourse.slicer.org/t/t1-and-dwi-co-registration-is-it-automatic/9272 "2020-02-25T22:10:50Z")
Operating system: Win 7 Pro Slicer version: 4.10.1 Expected behavior: N/A Actual behavior: N/A Hello everyone, New to Slicer - primarily interested in using it for DTI for now. I have downloaded dMRI and am going t… --- ## [Heart diffusion tensor exam](https://discourse.slicer.org/t/heart-diffusion-tensor-exam/10242)
**Author:** [@Pawel\_Ozga](https://discourse.slicer.org/u/Pawel_Ozga)\ **Replies:** 4\ **Last updated:** [February 17, 2020, 7:14pm UTC](https://discourse.slicer.org/t/heart-diffusion-tensor-exam/10242 "2020-02-17T19:14:12Z")
Hi, has anyone tried to make tractography out of heart DTI (not DWI) exams? Exam was made with 16 tensors and one direction. What’s worse the DTI include’s just a small part of chest while the ROI of structure sequence … --- ## [Problem with the gradients table in the data set](https://discourse.slicer.org/t/problem-with-the-gradients-table-in-the-data-set/10108)
**Author:** [@Santiago\_Cutiller](https://discourse.slicer.org/u/Santiago_Cutiller)\ **Replies:** 3\ **Last updated:** [February 5, 2020, 9:07pm UTC](https://discourse.slicer.org/t/problem-with-the-gradients-table-in-the-data-set/10108 "2020-02-05T21:07:09Z")
Hi! I am Santiago and I am working on a research project on epilepsy and diffusion tensor. I have a problem with the gradients table in the data set. When i trying use difussion brain masking I get the following error… --- ## [Optic Nerve tractography](https://discourse.slicer.org/t/optic-nerve-tractography/9993)
**Author:** [@HariES](https://discourse.slicer.org/u/HariES)\ **Replies:** 2\ **Last updated:** [January 29, 2020, 11:37pm UTC](https://discourse.slicer.org/t/optic-nerve-tractography/9993 "2020-01-29T23:37:20Z")
Dear Sir, Optic nerve is mixing with noise of image in the mask. So tensor is not estimated in dti estimation for the optic nerve. How to do optic nerve tracts after installing fiducial in optic nerve. --- ## [Intravoxel incoherent motion DWI?](https://discourse.slicer.org/t/intravoxel-incoherent-motion-dwi/9851)
**Author:** [@Striatum](https://discourse.slicer.org/u/Striatum)\ **Replies:** 1\ **Last updated:** [January 17, 2020, 5:05pm UTC](https://discourse.slicer.org/t/intravoxel-incoherent-motion-dwi/9851 "2020-01-17T17:05:47Z")
Is there a way to calculate IVIM f, D, D\* in Slicer from DWI DICOMs? I read some papers mentioning they used Slicer but I cannot find any clue. --- ## [Problem exporting Colorized tractography to PLY mesh](https://discourse.slicer.org/t/problem-exporting-colorized-tractography-to-ply-mesh/9768)
**Author:** [@tabildskov](https://discourse.slicer.org/u/tabildskov)\ **Replies:** 2\ **Last updated:** [January 13, 2020, 8:40pm UTC](https://discourse.slicer.org/t/problem-exporting-colorized-tractography-to-ply-mesh/9768 "2020-01-13T20:40:51Z")
Hello - While I can export the the tractography to a PLY mesh, the fiber bundle coloring does not always do what is expected. It always seems to color fibers by mean orientation not by segment orientation, not by tensor … [Previous page](https://discourse.slicer.org/c/community/slicerdmri/16.md) [Next page](https://discourse.slicer.org/c/community/slicerdmri/16.md?page=2)