# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=418

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

**Page:** 419

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## [Learning which data derivatives matter most (BIDS Derivatives Standardization)](https://discourse.slicer.org/t/learning-which-data-derivatives-matter-most-bids-derivatives-standardization/3430)

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**Author:** [@ihnorton](https://discourse.slicer.org/u/ihnorton)\
**Replies:** 0\
**Last updated:** [July 9, 2018, 2:30pm UTC](https://discourse.slicer.org/t/learning-which-data-derivatives-matter-most-bids-derivatives-standardization/3430 "2018-07-09T14:30:42Z")

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This message was sent to the old slicer-users list, and I’m re-posting here in case it is of interest. -@ihnorton Chris Gorgolewski krzysztof.gorgolewski@gmail.com via python.org 8:01 AM (2 hours ago) to bids-discussi…

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## [Save processed image as a DICOM series, in python](https://discourse.slicer.org/t/save-processed-image-as-a-dicom-series-in-python/3210)

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**Author:** [@gdenunzio](https://discourse.slicer.org/u/gdenunzio)\
**Replies:** 14\
**Last updated:** [July 7, 2018, 6:09pm UTC](https://discourse.slicer.org/t/save-processed-image-as-a-dicom-series-in-python/3210 "2018-07-07T18:09:36Z")

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Hi all, as it may be seen in my other post, “Rotation of a CT image around the RT isocenter, in python”, I have succeeded in applying a rotation to my DICOM volume. I still have to be sure that the rotation is around t…

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## [Local - adaptive Thresolding](https://discourse.slicer.org/t/local-adaptive-thresolding/3361)

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**Author:** [@mading](https://discourse.slicer.org/u/mading)\
**Replies:** 7\
**Last updated:** [July 7, 2018, 2:53pm UTC](https://discourse.slicer.org/t/local-adaptive-thresolding/3361 "2018-07-07T14:53:12Z")

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Dear all, I’m using 3D slicer for wooden objects. I need to extract accurate surfaces, and I did not get good results with global thresolding approaches (I mean the same grey value for all the object). Spruce wood is …

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## [Get total slice plane positions and orientation of CT volume in RAS?](https://discourse.slicer.org/t/get-total-slice-plane-positions-and-orientation-of-ct-volume-in-ras/3394)

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**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 4\
**Last updated:** [July 7, 2018, 4:57am UTC](https://discourse.slicer.org/t/get-total-slice-plane-positions-and-orientation-of-ct-volume-in-ras/3394 "2018-07-07T04:57:41Z")

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Hi Slicer developers. Excuse me to send this question. I have CT slices as 3D volume. How can I get the total axial slice plane positions and orientations in RAS coordinates using python interactor? Thanks for your gu…

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## [Scalar Volume Units?](https://discourse.slicer.org/t/scalar-volume-units/3405)

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**Author:** [@Masteling](https://discourse.slicer.org/u/Masteling)\
**Replies:** 3\
**Last updated:** [July 6, 2018, 8:17pm UTC](https://discourse.slicer.org/t/scalar-volume-units/3405 "2018-07-06T20:17:26Z")

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Hi all, When using the segment statistics module, besides the volume we get the minimum, maximum, mean and standard deviation of the segmentation. What are the units of the latest (min, max, means, std)? In the case o…

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## [DCE analysis - Fitted signal curve does not make sense](https://discourse.slicer.org/t/dce-analysis-fitted-signal-curve-does-not-make-sense/3403)

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**Author:** [@bmb777](https://discourse.slicer.org/u/bmb777)\
**Replies:** 3\
**Last updated:** [July 6, 2018, 3:05pm UTC](https://discourse.slicer.org/t/dce-analysis-fitted-signal-curve-does-not-make-sense/3403 "2018-07-06T15:05:27Z")

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Is the issue with the Output Fitted Data 4D a common issue? I believe I am having the same difficulty with viewing the fitted results as what is shown above and wonder if there is a way to fix/work around this. Specifica…

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## [DCE analysis - Ktrans is calculated only in a few small points](https://discourse.slicer.org/t/dce-analysis-ktrans-is-calculated-only-in-a-few-small-points/3402)

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**Author:** [@Egor](https://discourse.slicer.org/u/Egor)\
**Replies:** 1\
**Last updated:** [July 6, 2018, 3:02pm UTC](https://discourse.slicer.org/t/dce-analysis-ktrans-is-calculated-only-in-a-few-small-points/3402 "2018-07-06T15:02:22Z")

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How to get Ktrans from DCE multivolume? At random ROI level Ktrans is calculated only in a single small points

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## [The color of the flipped segment](https://discourse.slicer.org/t/the-color-of-the-flipped-segment/3400)

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**Author:** [@esurechao](https://discourse.slicer.org/u/esurechao)\
**Replies:** 2\
**Last updated:** [July 6, 2018, 2:58pm UTC](https://discourse.slicer.org/t/the-color-of-the-flipped-segment/3400 "2018-07-06T14:58:53Z")

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Operating system: windows 10 Slicer version: 4.9.0 I am trying to flip the segment of an organ in the 3D viewer. These are my steps: Load CT DICOM file. Use segment editor module to visualize the organ structure in …

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## [Residual paint on 3D view](https://discourse.slicer.org/t/residual-paint-on-3d-view/3393)

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**Author:** [@Charles\_Forsythe](https://discourse.slicer.org/u/Charles_Forsythe)\
**Replies:** 0\
**Last updated:** [July 5, 2018, 9:05pm UTC](https://discourse.slicer.org/t/residual-paint-on-3d-view/3393 "2018-07-05T21:05:27Z")

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Hello. I am using the ‘Paint’ and ‘Erase’ feautres on slicer and creating a 3D model. After painting and erasing all my slices, I click ‘Show 3D’ and I still have a few residual areas of paint on the 3D image but there …

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## [Import mhd data](https://discourse.slicer.org/t/import-mhd-data/3389)

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**Author:** [@weianlin](https://discourse.slicer.org/u/weianlin)\
**Replies:** 1\
**Last updated:** [July 5, 2018, 5:54pm UTC](https://discourse.slicer.org/t/import-mhd-data/3389 "2018-07-05T17:54:24Z")

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Hi, I’m new to 3D Slicer. I’d like to know how the mhd metadata would affect the image rendered in 3D Slicer. To my knowledge, 3D Slicer uses RAS coordinate system. And in mhd file, we can specify AnatomicalOrientation …

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## [Parsing CenterLine File (.vtk)](https://discourse.slicer.org/t/parsing-centerline-file-vtk/3384)

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**Author:** [@trnhx001](https://discourse.slicer.org/u/trnhx001)\
**Replies:** 2\
**Last updated:** [July 5, 2018, 2:32pm UTC](https://discourse.slicer.org/t/parsing-centerline-file-vtk/3384 "2018-07-05T14:32:28Z")

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Hi everyone, I am sorry to ask if this is a simple question. I am trying to parse the centerline file using python for data analysis, but I am confused about the coordinates in 3D Slicer. Is the data in world coordinat…

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## [Creating volume](https://discourse.slicer.org/t/creating-volume/3379)

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**Author:** [@Egor](https://discourse.slicer.org/u/Egor)\
**Replies:** 1\
**Last updated:** [July 5, 2018, 1:42pm UTC](https://discourse.slicer.org/t/creating-volume/3379 "2018-07-05T13:42:16Z")

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How to create volume without jagged lines and bands?

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## [transfrom to VTK data](https://discourse.slicer.org/t/transfrom-to-vtk-data/3385)

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**Author:** [@1102831521](https://discourse.slicer.org/u/1102831521)\
**Replies:** 1\
**Last updated:** [July 5, 2018, 1:28pm UTC](https://discourse.slicer.org/t/transfrom-to-vtk-data/3385 "2018-07-05T13:28:13Z")

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Operating system: WIN7 Slicer version: 4.8.1 Expected behavior: vtkMRMLNode data transfrom to VTK data Actual behavior:

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## [DICOM images to Inventor.](https://discourse.slicer.org/t/dicom-images-to-inventor/3382)

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**Author:** [@AlejandroDC](https://discourse.slicer.org/u/AlejandroDC)\
**Replies:** 1\
**Last updated:** [July 5, 2018, 1:22pm UTC](https://discourse.slicer.org/t/dicom-images-to-inventor/3382 "2018-07-05T13:22:18Z")

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Hi! I need to export DICOM images to jpeg for use in Inventor. I need to design the STL file in “real size” from DICOM images and i dont know how to export the images in real size from 3Dslicer. Thanks :slight\_smile:

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## [How to get the coordinates of intersection between vessel centerline and sequential MRI/CT slices in markup fiducials?](https://discourse.slicer.org/t/how-to-get-the-coordinates-of-intersection-between-vessel-centerline-and-sequential-mri-ct-slices-in-markup-fiducials/3016)

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**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 5\
**Last updated:** [July 4, 2018, 1:04pm UTC](https://discourse.slicer.org/t/how-to-get-the-coordinates-of-intersection-between-vessel-centerline-and-sequential-mri-ct-slices-in-markup-fiducials/3016 "2018-07-04T13:04:53Z")

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Hi Dear developers and users In the phantom study, I can segment vessel containing contrast agents in MRI and CT images using the option of “Level Set Segment” in the module of “Vascular Modeling Toolkit” with two point…

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## [Heatmaps on image slices and volume reconstruction](https://discourse.slicer.org/t/heatmaps-on-image-slices-and-volume-reconstruction/3301)

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**Author:** [@fmarcano1](https://discourse.slicer.org/u/fmarcano1)\
**Replies:** 1\
**Last updated:** [July 3, 2018, 10:50pm UTC](https://discourse.slicer.org/t/heatmaps-on-image-slices-and-volume-reconstruction/3301 "2018-07-03T22:50:08Z")

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Hello, Is there an usual way and examples in Slicer (using python) to add color maps to image slices and volume reconstructions?. I’ve found something similar to what I’d like do in a previous NA-MIC project week descri…

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## [invoking python CLI module from command line](https://discourse.slicer.org/t/invoking-python-cli-module-from-command-line/3369)

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**Author:** [@tjbertram](https://discourse.slicer.org/u/tjbertram)\
**Replies:** 1\
**Last updated:** [July 3, 2018, 10:30pm UTC](https://discourse.slicer.org/t/invoking-python-cli-module-from-command-line/3369 "2018-07-03T22:30:03Z")

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Operating system: macOS 10.13.2 (High Sierra) Slicer version: 4.8.1 Expected behavior: able to invoke python CLI module from command line Actual behavior: not able to invoke python CLI module from command line Greeti…

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## [Gamma Analysis of beam profiles](https://discourse.slicer.org/t/gamma-analysis-of-beam-profiles/3356)

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**Author:** [@AGul](https://discourse.slicer.org/u/AGul)\
**Replies:** 5\
**Last updated:** [July 3, 2018, 2:26pm UTC](https://discourse.slicer.org/t/gamma-analysis-of-beam-profiles/3356 "2018-07-03T14:26:25Z")

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Hi. How Can I calculate gamma index of two beam profiles acquired with to different detectors in 3D slicer. I have data in MS excel.

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## [How to know the dimensions of a 3D model using Slicer?](https://discourse.slicer.org/t/how-to-know-the-dimensions-of-a-3d-model-using-slicer/3115)

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**Author:** [@m.hilani](https://discourse.slicer.org/u/m.hilani)\
**Replies:** 4\
**Last updated:** [July 2, 2018, 8:41pm UTC](https://discourse.slicer.org/t/how-to-know-the-dimensions-of-a-3d-model-using-slicer/3115 "2018-07-02T20:41:10Z")

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Hello, I am performing tissue segmentation for 3D printing. I would like to know the volume of the end result 3D model and some of its dimensions to compare it with some reference measures from the literature. Is there…

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## [Build fails on Ubuntu 14.04](https://discourse.slicer.org/t/build-fails-on-ubuntu-14-04/3330)

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**Author:** [@Lorensen](https://discourse.slicer.org/u/Lorensen)\
**Replies:** 5\
**Last updated:** [July 2, 2018, 6:03pm UTC](https://discourse.slicer.org/t/build-fails-on-ubuntu-14-04/3330 "2018-07-02T18:03:03Z")

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%\] Built target python-appdirs \[ 20%\] No configure step for ‘python-pyparsing’ \[ 20%\] No build step for ‘python-pyparsing’ \[ 21%\] Performing install step for ‘python-pyparsing’ Traceback (most recent call last): Fil…

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## [Visualize BRAINS control points](https://discourse.slicer.org/t/visualize-brains-control-points/2359)

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**Author:** [@hadasara](https://discourse.slicer.org/u/hadasara)\
**Replies:** 11\
**Last updated:** [March 19, 2018, 7:53pm UTC](https://discourse.slicer.org/t/visualize-brains-control-points/2359 "2018-03-19T19:53:30Z")

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Hi, I’m new in 3dslicer. I would like to know if and how I can see the control points in BRAINS non-rigid B-spline registration. Where they are located in my images, and where the locked points are located. I think that…

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## [Details on ICP registration implementation](https://discourse.slicer.org/t/details-on-icp-registration-implementation/3343)

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**Author:** [@odiseo123](https://discourse.slicer.org/u/odiseo123)\
**Replies:** 1\
**Last updated:** [July 1, 2018, 1:48pm UTC](https://discourse.slicer.org/t/details-on-icp-registration-implementation/3343 "2018-07-01T13:48:24Z")

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Operating system: Windows 7 64bits Slicer version: 4.8.1 Expected behavior: N/A Actual behavior: N/A I am using the surface registration module with “Surface Registration” as “Type of Registration”. I just wanted som…

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## [Determining the fat percentage of a tumor on CT? ](https://discourse.slicer.org/t/determining-the-fat-percentage-of-a-tumor-on-ct/3350)

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**Author:** [@SMR](https://discourse.slicer.org/u/SMR)\
**Replies:** 1\
**Last updated:** [July 1, 2018, 1:22pm UTC](https://discourse.slicer.org/t/determining-the-fat-percentage-of-a-tumor-on-ct/3350 "2018-07-01T13:22:16Z")

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I’m basically trying to quantity the fat percentage of tumors on CT, any suggestions on how to do this in 3D slicer would be very much appreciated.

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## [MIP in 3D viewing panel isn't matching MIP in slice viewer](https://discourse.slicer.org/t/mip-in-3d-viewing-panel-isnt-matching-mip-in-slice-viewer/3347)

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**Author:** [@Hamburgerfinger](https://discourse.slicer.org/u/Hamburgerfinger)\
**Replies:** 1\
**Last updated:** [June 30, 2018, 10:48pm UTC](https://discourse.slicer.org/t/mip-in-3d-viewing-panel-isnt-matching-mip-in-slice-viewer/3347 "2018-06-30T22:48:06Z")

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Hi Slicers! I’m having a little trouble understanding why, when I’m using the maximum intensity projection rendering method in the 3D viewer, the image doesn’t exactly match (it’s pretty close) a MIP generated in the sl…

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## [Validity of the 3D slicer software](https://discourse.slicer.org/t/validity-of-the-3d-slicer-software/3341)

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**Author:** [@Mohamed1982](https://discourse.slicer.org/u/Mohamed1982)\
**Replies:** 1\
**Last updated:** [June 30, 2018, 1:38pm UTC](https://discourse.slicer.org/t/validity-of-the-3d-slicer-software/3341 "2018-06-30T13:38:47Z")

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Hi I have a project about the 3D slicer software in the assessment of the olfactory bulb volume, but I want to ask if there is any article for the validation of this software and if there are studies comparing results …

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## [New Guy With ROI Question](https://discourse.slicer.org/t/new-guy-with-roi-question/3321)

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**Author:** [@Zenbiker](https://discourse.slicer.org/u/Zenbiker)\
**Replies:** 2\
**Last updated:** [June 29, 2018, 5:52pm UTC](https://discourse.slicer.org/t/new-guy-with-roi-question/3321 "2018-06-29T17:52:19Z")

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Trying to create .stl file from ROI created: DICOM, Volume Rendering, Editor/Make Model. When I select Make Model, the entire volume reappears attahed to the ROI and the .stl file is a representation of the entire volum…

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## [Reslicing a series of DICOM images and exporting them](https://discourse.slicer.org/t/reslicing-a-series-of-dicom-images-and-exporting-them/3328)

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**Author:** [@tehm0n](https://discourse.slicer.org/u/tehm0n)\
**Replies:** 0\
**Last updated:** [June 28, 2018, 2:04pm UTC](https://discourse.slicer.org/t/reslicing-a-series-of-dicom-images-and-exporting-them/3328 "2018-06-28T14:04:44Z")

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Hi! I have imported a series of DICOM files containing 2D MR images. These MR slices are located in the axial plane at locations -40.063mm to -0.063mm in 4mm intervals. I want to reslice this series to have slicelocatio…

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## [Unable to apply segment statistic](https://discourse.slicer.org/t/unable-to-apply-segment-statistic/3316)

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**Author:** [@Ash\_Alarfaj](https://discourse.slicer.org/u/Ash_Alarfaj)\
**Replies:** 1\
**Last updated:** [June 28, 2018, 12:41am UTC](https://discourse.slicer.org/t/unable-to-apply-segment-statistic/3316 "2018-06-28T00:41:09Z")

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Problem report for Slicer 4.8.1 macosx-amd64: \[please describe expected and actual behavior\] after I’ve finished segmentation and added names for segment and table the apply icon didn’t work.

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## [Save derived DTI heatmap](https://discourse.slicer.org/t/save-derived-dti-heatmap/3319)

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**Author:** [@ssyip](https://discourse.slicer.org/u/ssyip)\
**Replies:** 1\
**Last updated:** [June 27, 2018, 6:38pm UTC](https://discourse.slicer.org/t/save-derived-dti-heatmap/3319 "2018-06-27T18:38:53Z")

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## [Exporting a DTI object as a 3D File](https://discourse.slicer.org/t/exporting-a-dti-object-as-a-3d-file/987)

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**Author:** [@vascopontinha](https://discourse.slicer.org/u/vascopontinha)\
**Replies:** 9\
**Last updated:** [May 2, 2018, 12:45pm UTC](https://discourse.slicer.org/t/exporting-a-dti-object-as-a-3d-file/987 "2018-05-02T12:45:53Z")

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Operating system: macOS Slicer version: 4.3 & 4.7 Hi everyone, While I was building a tractography display, Slicer allows me to export it as a \*.obj file, however, it fails to export the labels file. Thus, when I try …

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