# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=429

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

**Page:** 430

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## [How to load 4D images in Slicer - fMRI or ASL datasets](https://discourse.slicer.org/t/how-to-load-4d-images-in-slicer-fmri-or-asl-datasets/1157)

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**Author:** [@acsenrafilho](https://discourse.slicer.org/u/acsenrafilho)\
**Replies:** 23\
**Last updated:** [March 16, 2018, 12:14am UTC](https://discourse.slicer.org/t/how-to-load-4d-images-in-slicer-fmri-or-asl-datasets/1157 "2018-03-16T00:14:19Z")

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Hello, slicers! Firstly, I am sorry if this is a naive question, but I’ve tried to find something on the web and until now I could not fix my problem. I have a small dataset with ASL and fMRI (both as 4D nii files) whi…

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## [Intensities histogram of a segmented area](https://discourse.slicer.org/t/intensities-histogram-of-a-segmented-area/2164)

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**Author:** [@Diana](https://discourse.slicer.org/u/Diana)\
**Replies:** 16\
**Last updated:** [March 16, 2018, 12:10am UTC](https://discourse.slicer.org/t/intensities-histogram-of-a-segmented-area/2164 "2018-03-16T00:10:34Z")

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Hello, please is there any way, how to get the histogram of intensities of only a bordered area by segmentation? I am working with MRI scans, one is 3D and serves for the segmantation of an organ and the second, which i…

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## [Image Origin mismatch: DICOM viewer vs. SLICER](https://discourse.slicer.org/t/image-origin-mismatch-dicom-viewer-vs-slicer/2307)

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**Author:** [@dcantor](https://discourse.slicer.org/u/dcantor)\
**Replies:** 11\
**Last updated:** [March 15, 2018, 10:45pm UTC](https://discourse.slicer.org/t/image-origin-mismatch-dicom-viewer-vs-slicer/2307 "2018-03-15T22:45:35Z")

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Hi Slicers, I am writing a python script to convert from DICOM to NRRD so I am going through the different DICOM headers and I am calculating the Image Origin of my T2W volume. After sorting the list of DICOM slices acc…

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## [How Can I Convert VTK file to nifti format?](https://discourse.slicer.org/t/how-can-i-convert-vtk-file-to-nifti-format/1034)

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**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 3\
**Last updated:** [September 11, 2017, 5:25pm UTC](https://discourse.slicer.org/t/how-can-i-convert-vtk-file-to-nifti-format/1034 "2017-09-11T17:25:55Z")

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Hi users and developes of Slicer For creating surface model from one nifti image file, I used “Grayscale Model Maker” module in the category of “Surface Models”. I can save this surface model in vtk format successfully. …

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## [Segmentation leaves empty vertical lines](https://discourse.slicer.org/t/segmentation-leaves-empty-vertical-lines/2319)

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**Author:** [@alessandronavacchia](https://discourse.slicer.org/u/alessandronavacchia)\
**Replies:** 2\
**Last updated:** [March 15, 2018, 2:22pm UTC](https://discourse.slicer.org/t/segmentation-leaves-empty-vertical-lines/2319 "2018-03-15T14:22:42Z")

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Hi all, I am having trouble with segmenting an MRI. I am using the ‘draw’ tool in the ‘Segment editor’. I draw the outline you can see in this picture: And when I press enter, this is what I get: As you can see,…

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## [Segmentation of mrml file in different machine have different resolution](https://discourse.slicer.org/t/segmentation-of-mrml-file-in-different-machine-have-different-resolution/2305)

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**Author:** [@Masteling](https://discourse.slicer.org/u/Masteling)\
**Replies:** 11\
**Last updated:** [March 14, 2018, 9:24pm UTC](https://discourse.slicer.org/t/segmentation-of-mrml-file-in-different-machine-have-different-resolution/2305 "2018-03-14T21:24:09Z")

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Hi, I tried to segment the same mrml file in 2 different computers (created file in machine 1 and copied to machine 2 before segmenting) and the segmentation resolution if different between those machines. Machine 1: p…

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## [Surface similarity of a model](https://discourse.slicer.org/t/surface-similarity-of-a-model/2287)

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**Author:** [@Joelle](https://discourse.slicer.org/u/Joelle)\
**Replies:** 3\
**Last updated:** [March 14, 2018, 6:11pm UTC](https://discourse.slicer.org/t/surface-similarity-of-a-model/2287 "2018-03-14T18:11:33Z")

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Hi I got an image of a person and my goal is to compare the left and the right side of the face and get the similarity or difference of it’s surface. Best would be to only compare a region of interest. This is an examp…

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## [Source of sample data  "Full head MRI scan"](https://discourse.slicer.org/t/source-of-sample-data-full-head-mri-scan/2316)

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**Author:** [@Yuan](https://discourse.slicer.org/u/Yuan)\
**Replies:** 1\
**Last updated:** [March 14, 2018, 4:27pm UTC](https://discourse.slicer.org/t/source-of-sample-data-full-head-mri-scan/2316 "2018-03-14T16:27:01Z")

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I would like to refer to the sample data “Full head MRI scan”. I wonder is the source information of this data available? Is it from a subject or averaged from several subjects and any information of the subject or the s…

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## [Slicer save function creating copies of dataset instead of overwrite](https://discourse.slicer.org/t/slicer-save-function-creating-copies-of-dataset-instead-of-overwrite/2311)

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**Author:** [@drusmanbashir](https://discourse.slicer.org/u/drusmanbashir)\
**Replies:** 1\
**Last updated:** [March 14, 2018, 12:50pm UTC](https://discourse.slicer.org/t/slicer-save-function-creating-copies-of-dataset-instead-of-overwrite/2311 "2018-03-14T12:50:40Z")

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Hi, I am not sure if this is how it is supposed to work. But when i load the data folder i saved previously, slicer creates copies of all files and assigns them a suffix like ‘\_1’ . If I were to save the data again afte…

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## [Error when using Endoscopy module](https://discourse.slicer.org/t/error-when-using-endoscopy-module/2286)

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**Author:** [@hherhold](https://discourse.slicer.org/u/hherhold)\
**Replies:** 3\
**Last updated:** [March 13, 2018, 2:56pm UTC](https://discourse.slicer.org/t/error-when-using-endoscopy-module/2286 "2018-03-13T14:56:41Z")

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Hi, Getting an error when using Endoscopy module in master build. I loaded in a volume, and through various manipulations, wound up with about 7 default cameras. I went in to “Data” and deleted all but one default camer…

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## [Affine matrices (Insight format) with tag MatrixOffsetTransformBase\_double\_3\_3 cannot be loaded into Slicer anymore](https://discourse.slicer.org/t/affine-matrices-insight-format-with-tag-matrixoffsettransformbase-double-3-3-cannot-be-loaded-into-slicer-anymore/2302)

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**Author:** [@mangotee](https://discourse.slicer.org/u/mangotee)\
**Replies:** 2\
**Last updated:** [March 13, 2018, 1:38pm UTC](https://discourse.slicer.org/t/affine-matrices-insight-format-with-tag-matrixoffsettransformbase-double-3-3-cannot-be-loaded-into-slicer-anymore/2302 "2018-03-13T13:38:19Z")

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After running ANTs buildtemplateparallel.sh script to create a template from several of our MRI scans, we receive multiple pairs of linear-affine matrices (.txt) and deformation fields (.nii.gz) that I want to load into …

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## [Sphere smoothing](https://discourse.slicer.org/t/sphere-smoothing/2301)

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**Author:** [@nodi](https://discourse.slicer.org/u/nodi)\
**Replies:** 1\
**Last updated:** [March 13, 2018, 12:11pm UTC](https://discourse.slicer.org/t/sphere-smoothing/2301 "2018-03-13T12:11:02Z")

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I draw number of spheres and it looks ugly. need smoothing. I don’t know how to do that. could you please advice me?

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## [Invoke N4ITK Bias Correction Programmatically](https://discourse.slicer.org/t/invoke-n4itk-bias-correction-programmatically/2300)

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**Author:** [@zjx1805](https://discourse.slicer.org/u/zjx1805)\
**Replies:** 2\
**Last updated:** [March 12, 2018, 6:35pm UTC](https://discourse.slicer.org/t/invoke-n4itk-bias-correction-programmatically/2300 "2018-03-12T18:35:45Z")

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Hello All, Is there a way to programmatically invoke the N4ITKBiasCorrection module through the python interpreter? I was trying to figure out what parameters as well as their types I need to provide by looking at the s…

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## [CT slices are not stacked on top of each other](https://discourse.slicer.org/t/ct-slices-are-not-stacked-on-top-of-each-other/2299)

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**Author:** [@ReNeu](https://discourse.slicer.org/u/ReNeu)\
**Replies:** 1\
**Last updated:** [March 12, 2018, 3:56pm UTC](https://discourse.slicer.org/t/ct-slices-are-not-stacked-on-top-of-each-other/2299 "2018-03-12T15:56:07Z")

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Hi Andras, Another problem that I have encountered while loading a file of CT images is that they don’t stack on top of each other. This does not occur when viewing the images outside Slicer. I’ve tried attaching scree…

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## [Rotate 3D image](https://discourse.slicer.org/t/rotate-3d-image/1968)

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**Author:** [@Ahmed\_Soufane](https://discourse.slicer.org/u/Ahmed_Soufane)\
**Replies:** 11\
**Last updated:** [March 12, 2018, 3:51pm UTC](https://discourse.slicer.org/t/rotate-3d-image/1968 "2018-03-12T15:51:06Z")

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How to rotate the 3D image using phython interactor ?

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## [cannot manually install extension on mac](https://discourse.slicer.org/t/cannot-manually-install-extension-on-mac/2280)

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**Author:** [@mgastall](https://discourse.slicer.org/u/mgastall)\
**Replies:** 2\
**Last updated:** [March 12, 2018, 1:56pm UTC](https://discourse.slicer.org/t/cannot-manually-install-extension-on-mac/2280 "2018-03-12T13:56:17Z")

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Trying to manually install radionomics extension. I followed instructions, and under module settings I added from the extension folder: /Applications/27030-win-amd64-SlicerRadiomics-git0c693c5-2018-03-07/Lib/Slicer-4.9…

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## [Measure tumor and edema volume](https://discourse.slicer.org/t/measure-tumor-and-edema-volume/2290)

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**Author:** [@joaomarto](https://discourse.slicer.org/u/joaomarto)\
**Replies:** 1\
**Last updated:** [March 12, 2018, 5:42am UTC](https://discourse.slicer.org/t/measure-tumor-and-edema-volume/2290 "2018-03-12T05:42:25Z")

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Hello, I am using for the first time the 3D slicer software and I am having difficulty in calculating cerebral tumors volumes. Also I would link to measure the surrounding edema volume. What is the best way to do it? T…

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## [No volumes to visualise from CT scan](https://discourse.slicer.org/t/no-volumes-to-visualise-from-ct-scan/1127)

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**Author:** [@John\_D](https://discourse.slicer.org/u/John_D)\
**Replies:** 3\
**Last updated:** [September 26, 2017, 11:59pm UTC](https://discourse.slicer.org/t/no-volumes-to-visualise-from-ct-scan/1127 "2017-09-26T23:59:15Z")

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I am looking at this tutorial: https://www.slicer.org/wiki/Documentation/4.3/Modules/VolumeRendering I have loaded DICOM data for a CT scan - added the files and then clicked Load in DICOM panel - and it is displaying …

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## [Rotation&zooming ](https://discourse.slicer.org/t/rotation-zooming/1912)

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**Author:** [@Ahmed\_Soufane](https://discourse.slicer.org/u/Ahmed_Soufane)\
**Replies:** 12\
**Last updated:** [March 11, 2018, 4:32am UTC](https://discourse.slicer.org/t/rotation-zooming/1912 "2018-03-11T04:32:12Z")

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Hello, How can I modify or call the rotation of an image on the python interactor on 3dslicer ? Is it possible to modify or edit zooming in and out of the image on python console ?

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## [slicerIGT extension](https://discourse.slicer.org/t/slicerigt-extension/2278)

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**Author:** [@Vinny](https://discourse.slicer.org/u/Vinny)\
**Replies:** 2\
**Last updated:** [March 11, 2018, 2:45am UTC](https://discourse.slicer.org/t/slicerigt-extension/2278 "2018-03-11T02:45:12Z")

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Hi, When using Slicer 4.9.0 2018-01-22 version, SlicerIGT cannot be found in the Extensions Manager. I get this message: No extensions found for win:64-bit, revision: ‘26853’. Please try a different combination Howev…

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## [Real-time distance measurement between the needle tip and target with PlusToolkit and 3D Slicer](https://discourse.slicer.org/t/real-time-distance-measurement-between-the-needle-tip-and-target-with-plustoolkit-and-3d-slicer/1611)

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**Author:** [@Serg](https://discourse.slicer.org/u/Serg)\
**Replies:** 9\
**Last updated:** [March 11, 2018, 2:41am UTC](https://discourse.slicer.org/t/real-time-distance-measurement-between-the-needle-tip-and-target-with-plustoolkit-and-3d-slicer/1611 "2018-03-11T02:41:15Z")

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Operating system: Slicer version: Expected behavior: Actual behavior: I’m a newbie in 3d Slicer and amazed its functionality. Great work! I’m looking for the solution to dynamically measure the distance between the …

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## [Python Interactor process](https://discourse.slicer.org/t/python-interactor-process/2283)

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**Author:** [@Fadwa\_Darwaish](https://discourse.slicer.org/u/Fadwa_Darwaish)\
**Replies:** 1\
**Last updated:** [March 10, 2018, 10:13pm UTC](https://discourse.slicer.org/t/python-interactor-process/2283 "2018-03-10T22:13:33Z")

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I would like to know the process name/number to link to the Python interactor Thank you Fadwa

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## ["Transform Hierarchy" in data module not showing multiple transforms correctly](https://discourse.slicer.org/t/transform-hierarchy-in-data-module-not-showing-multiple-transforms-correctly/2153)

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**Author:** [@Nathan](https://discourse.slicer.org/u/Nathan)\
**Replies:** 11\
**Last updated:** [March 10, 2018, 6:26pm UTC](https://discourse.slicer.org/t/transform-hierarchy-in-data-module-not-showing-multiple-transforms-correctly/2153 "2018-03-10T18:26:24Z")

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Hello, I just updated to Slicer 4.8.1 and noticed that the “Transform hierarchy” is not behaving correctly. It does not show the correct “tree” of transformations. For example, I have images that have four transformatio…

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## [Fly-through rendering](https://discourse.slicer.org/t/fly-through-rendering/1947)

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**Author:** [@nirotu](https://discourse.slicer.org/u/nirotu)\
**Replies:** 3\
**Last updated:** [March 10, 2018, 1:18am UTC](https://discourse.slicer.org/t/fly-through-rendering/1947 "2018-03-10T01:18:08Z")

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Hello: I am trying to use mesh file in MAYA software to create fly-though anatomic image. BTW, is it possible to create fly-though within 3D Slicer itself? Trying to avoid going to MAYA. The mesh tile was created usi…

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## [Surface representation of segmentation is too much smoothed](https://discourse.slicer.org/t/surface-representation-of-segmentation-is-too-much-smoothed/2277)

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**Author:** [@mete\_naz](https://discourse.slicer.org/u/mete_naz)\
**Replies:** 1\
**Last updated:** [March 9, 2018, 9:05pm UTC](https://discourse.slicer.org/t/surface-representation-of-segmentation-is-too-much-smoothed/2277 "2018-03-09T21:05:04Z")

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Hi! I have been doing segmentation for EAT and Ventricles. I use manual segmentation by hand. Whenever I look at the 3D Model generated by 3D Slicer, I see that there are gaps between slices even if I segmented every sl…

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## [Multiple monitors](https://discourse.slicer.org/t/multiple-monitors/2250)

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**Author:** [@Jason\_Gellis](https://discourse.slicer.org/u/Jason_Gellis)\
**Replies:** 3\
**Last updated:** [March 8, 2018, 5:16pm UTC](https://discourse.slicer.org/t/multiple-monitors/2250 "2018-03-08T17:16:05Z")

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Is there any way to split the red, green, yellow, and 3d screen to another monitor? It would be nice to keep the modules on one screen and images on another. Thank you.

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## [No 4.8.1 extensions builds on Mac since Feb 22](https://discourse.slicer.org/t/no-4-8-1-extensions-builds-on-mac-since-feb-22/2259)

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**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 2\
**Last updated:** [March 8, 2018, 2:53pm UTC](https://discourse.slicer.org/t/no-4-8-1-extensions-builds-on-mac-since-feb-22/2259 "2018-03-08T14:53:00Z")

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There are no mac builds of extensions starting Feb 23. Is this expected? cc: @JoostJM

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## [Handle/hole identification and navigation in segmentation MRI volume](https://discourse.slicer.org/t/handle-hole-identification-and-navigation-in-segmentation-mri-volume/2262)

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**Author:** [@JvD](https://discourse.slicer.org/u/JvD)\
**Replies:** 2\
**Last updated:** [March 8, 2018, 11:23am UTC](https://discourse.slicer.org/t/handle-hole-identification-and-navigation-in-segmentation-mri-volume/2262 "2018-03-08T11:23:53Z")

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Dear all, I am working with brain MRI data in Slicer 4.4.0 on Ubuntu 14.04. I have automatically generated gray/white matter segmentations that I need to correct for miss classifications, and especially handles (loops …

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## [Radiomics module crashes anytime I use a "Theta parameter map"](https://discourse.slicer.org/t/radiomics-module-crashes-anytime-i-use-a-theta-parameter-map/2152)

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**Author:** [@Andrea\_Barucci1](https://discourse.slicer.org/u/Andrea_Barucci1)\
**Replies:** 18\
**Last updated:** [March 7, 2018, 4:25pm UTC](https://discourse.slicer.org/t/radiomics-module-crashes-anytime-i-use-a-theta-parameter-map/2152 "2018-03-07T16:25:02Z")

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Hi, good morning to everyone and sorry if my question has a solution in thread I have not found. My problem is simple: Eveytime I’m trying to evaluate radionics features using a diffusion map obtained by the DWModelin…

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## [Fine-tuning linking function between windows](https://discourse.slicer.org/t/fine-tuning-linking-function-between-windows/2258)

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**Author:** [@drusmanbashir](https://discourse.slicer.org/u/drusmanbashir)\
**Replies:** 2\
**Last updated:** [March 7, 2018, 4:02pm UTC](https://discourse.slicer.org/t/fine-tuning-linking-function-between-windows/2258 "2018-03-07T16:02:13Z")

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Hi, Osirix has a handy function that allows you to manually set up your windows with any adjusted windowing, zoom, and position and then when you link the windows it preserves those transformations in each window. E.g.,…

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