# Support **URL:** https://discourse.slicer.org/c/support/11.md?page=358 [Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md) **Page:** 359 --- ## [Cannot paint segments outside a certain region in an MRI image](https://discourse.slicer.org/t/cannot-paint-segments-outside-a-certain-region-in-an-mri-image/9710)
**Author:** [@momosukh](https://discourse.slicer.org/u/momosukh)\ **Replies:** 1\ **Last updated:** [January 5, 2020, 4:07am UTC](https://discourse.slicer.org/t/cannot-paint-segments-outside-a-certain-region-in-an-mri-image/9710 "2020-01-05T04:07:19Z")
I am facing a weird issue, I am unable to paint the layer of the outer abdomen, fat, using paint, draw, and other techniques, as shown as the red circle in the figure. The ROI of the area is well spaced in all 3 coordina… --- ## [Converting fiducial coordinates from RAS to LPS](https://discourse.slicer.org/t/converting-fiducial-coordinates-from-ras-to-lps/9707)
**Author:** [@matt-warkentin](https://discourse.slicer.org/u/matt-warkentin)\ **Replies:** 6\ **Last updated:** [January 4, 2020, 12:37am UTC](https://discourse.slicer.org/t/converting-fiducial-coordinates-from-ras-to-lps/9707 "2020-01-04T00:37:38Z")
Hi, I am working with some chest CT scans and I have some fiducials which denote the 3D centre of a tumour mass. I have saved/exported the fiducials from Slicer as .fcsv files. I have done some searching online but I a… --- ## [How to segment all pores and its connecting paths seperately ](https://discourse.slicer.org/t/how-to-segment-all-pores-and-its-connecting-paths-seperately/9525)
**Author:** [@muntahi398](https://discourse.slicer.org/u/muntahi398)\ **Replies:** 15\ **Last updated:** [January 3, 2020, 7:32pm UTC](https://discourse.slicer.org/t/how-to-segment-all-pores-and-its-connecting-paths-seperately/9525 "2020-01-03T19:32:21Z")
Dear altruists, I am trying to segment this 3d binary volume of having many spherical blobs connected to one another with some small path. Can you suggest me simple way of segmenting all the pores individually and sep… --- ## [How to load TIFF image stacks that don't have scalar overlay already associated?](https://discourse.slicer.org/t/how-to-load-tiff-image-stacks-that-dont-have-scalar-overlay-already-associated/9679)
**Author:** [@carterrt](https://discourse.slicer.org/u/carterrt)\ **Replies:** 12\ **Last updated:** [January 3, 2020, 5:43pm UTC](https://discourse.slicer.org/t/how-to-load-tiff-image-stacks-that-dont-have-scalar-overlay-already-associated/9679 "2020-01-03T17:43:08Z")
I have a few TIFF image stacks that when I load into Slicer seem to only have a volume data set and no scalar overlay data associated with them and therefore load in an illogical way. When I load different TIFF image sta… --- ## [So weirdly slicer always erases 1 slice lower... WHY?!](https://discourse.slicer.org/t/so-weirdly-slicer-always-erases-1-slice-lower-why/9697)
**Author:** [@NoobForSlicer](https://discourse.slicer.org/u/NoobForSlicer)\ **Replies:** 10\ **Last updated:** [January 3, 2020, 4:12pm UTC](https://discourse.slicer.org/t/so-weirdly-slicer-always-erases-1-slice-lower-why/9697 "2020-01-03T16:12:44Z")
There is always a problem, I set everything okay but for some unknown reason, slicer is painting 1 slice lower. Here is the image. Yellow line is my eraser tool. When I click as you can see, it erased one slice lower. … --- ## [Inaccurate volume measurement](https://discourse.slicer.org/t/inaccurate-volume-measurement/9702)
**Author:** [@Hansveerman](https://discourse.slicer.org/u/Hansveerman)\ **Replies:** 3\ **Last updated:** [January 3, 2020, 1:54pm UTC](https://discourse.slicer.org/t/inaccurate-volume-measurement/9702 "2020-01-03T13:54:14Z")
Hi all, I am new to 3Dslicer. I loaded prostate MRI images with 3mm slice thickness. Then i tried to check the accuracy of the volume measurement option before I did any other calculations. When i create spherical st… --- ## [Expanding volume without squeezing others](https://discourse.slicer.org/t/expanding-volume-without-squeezing-others/9704)
**Author:** [@annigilus](https://discourse.slicer.org/u/annigilus)\ **Replies:** 1\ **Last updated:** [January 3, 2020, 1:36pm UTC](https://discourse.slicer.org/t/expanding-volume-without-squeezing-others/9704 "2020-01-03T13:36:59Z")
How can I expand one volume without squeezing others volumes nearby? Can I overlap volumes one to another? And hov can I combine two different volumes to the one new? (For example, I have two volumes of femoral heads na… --- ## [Expanding of volume](https://discourse.slicer.org/t/expanding-of-volume/9696)
**Author:** [@annigilus](https://discourse.slicer.org/u/annigilus)\ **Replies:** 1\ **Last updated:** [January 3, 2020, 1:59am UTC](https://discourse.slicer.org/t/expanding-of-volume/9696 "2020-01-03T01:59:38Z")
How can I expand borders of segment volume to defiend margin (1 cm for example) by single command? --- ## [Can't get it to install on my Chromebook](https://discourse.slicer.org/t/cant-get-it-to-install-on-my-chromebook/9668)
**Author:** [@Logan\_Quinn](https://discourse.slicer.org/u/Logan_Quinn)\ **Replies:** 7\ **Last updated:** [January 2, 2020, 7:13pm UTC](https://discourse.slicer.org/t/cant-get-it-to-install-on-my-chromebook/9668 "2020-01-02T19:13:43Z")
Operating system: Version 79.0.3945.86 (Official Build) (64-bit) Using the Linux (beta) feature. Slicer version: 4.10.2 Expected behavior: Following instruction at https://www.slicer.org/wiki/Documentation/4.10/FAQ#How… --- ## [Omitting the rotation of needle around its axis in the transformation module](https://discourse.slicer.org/t/omitting-the-rotation-of-needle-around-its-axis-in-the-transformation-module/8247)
**Author:** [@Mary7291](https://discourse.slicer.org/u/Mary7291)\ **Replies:** 1\ **Last updated:** [August 31, 2019, 4:38pm UTC](https://discourse.slicer.org/t/omitting-the-rotation-of-needle-around-its-axis-in-the-transformation-module/8247 "2019-08-31T16:38:06Z")
Operating system: window 7 Slicer version:4.8.1 Hello, To plan a needle insertion process, i need to load a needle in slicer and finding the transformation of the needle to obtain the position and orientation if the n… --- ## [Missing menu items from Slicer Application Main Window](https://discourse.slicer.org/t/missing-menu-items-from-slicer-application-main-window/2613)
**Author:** [@Andinet\_Enquobahrie](https://discourse.slicer.org/u/Andinet_Enquobahrie)\ **Replies:** 3\ **Last updated:** [January 2, 2020, 6:00pm UTC](https://discourse.slicer.org/t/missing-menu-items-from-slicer-application-main-window/2613 "2020-01-02T18:00:27Z")
Hi, I downloaded the nightly Windows installer and installed it on my Windows 10 Pro laptop. Slicer’s Main Application menu seems to be missing (File, Edit, View and Help). see below My laptop system information ca… --- ## [Show ruler name and length in slice view](https://discourse.slicer.org/t/show-ruler-name-and-length-in-slice-view/9688)
**Author:** [@torquil](https://discourse.slicer.org/u/torquil)\ **Replies:** 1\ **Last updated:** [January 2, 2020, 3:29pm UTC](https://discourse.slicer.org/t/show-ruler-name-and-length-in-slice-view/9688 "2020-01-02T15:29:37Z")
If I do not remember incorrectly, it was possible before to see the ruler name and length in the slice view. Now I can only see it in the 3D view. How can I get the slice view to show the ruler name and length? Using th… --- ## [SlicerRT creating volume](https://discourse.slicer.org/t/slicerrt-creating-volume/9677)
**Author:** [@annigilus](https://discourse.slicer.org/u/annigilus)\ **Replies:** 1\ **Last updated:** [January 1, 2020, 5:51pm UTC](https://discourse.slicer.org/t/slicerrt-creating-volume/9677 "2020-01-01T17:51:54Z")
Greetings, everyone! And Happy New Year! I have a question: how can I create new volumes in my dicom series in Slicer (CTV, PTV, OAR) to calculate the dose on this particular volume? (Worked in PLUNC, it has such tool. … --- ## [Hardware connection for IGT](https://discourse.slicer.org/t/hardware-connection-for-igt/5825)
**Author:** [@Felix\_Navarro\_Guirad](https://discourse.slicer.org/u/Felix_Navarro_Guirad)\ **Replies:** 5\ **Last updated:** [January 1, 2020, 6:34am UTC](https://discourse.slicer.org/t/hardware-connection-for-igt/5825 "2020-01-01T06:34:43Z")
Dear communuty, We are trying to connect our ultrasound device and brachy stepper to Slicer using the PLUS server. Do any of you have used a BK US device (via OEM interface or video capture) or a brachy stepper as trac… --- ## [How to show VR in View2/3 by code?](https://discourse.slicer.org/t/how-to-show-vr-in-view2-3-by-code/9671)
**Author:** [@apparrilla](https://discourse.slicer.org/u/apparrilla)\ **Replies:** 2\ **Last updated:** [December 31, 2019, 3:23pm UTC](https://discourse.slicer.org/t/how-to-show-vr-in-view2-3-by-code/9671 "2019-12-31T15:23:54Z")
How can I switch on/off volume rendering in secondary views by code? Thanks! --- ## [Whole brain segmentation registration ](https://discourse.slicer.org/t/whole-brain-segmentation-registration/9663)
**Author:** [@DanTran](https://discourse.slicer.org/u/DanTran)\ **Replies:** 3\ **Last updated:** [December 31, 2019, 3:50am UTC](https://discourse.slicer.org/t/whole-brain-segmentation-registration/9663 "2019-12-31T03:50:12Z")
Hi, my project consists of fully segmenting non-human brains ex-vivo in order to compute difference in the volume of brain tissue between pre and postoperative conditions. My questions are: what format should I use to … --- ## [Automating segmentation on volumes](https://discourse.slicer.org/t/automating-segmentation-on-volumes/2741)
**Author:** [@slojanko](https://discourse.slicer.org/u/slojanko)\ **Replies:** 19\ **Last updated:** [December 30, 2019, 4:36pm UTC](https://discourse.slicer.org/t/automating-segmentation-on-volumes/2741 "2019-12-30T16:36:02Z")
Hello, I’ve started using Slicer a few weeks ago for a University project. It’s about segmenting the volume of a cell with a predefined (known parameters) threshold, smoothing, removing small islands and margin increase… --- ## [Philips EPIQ 7 vol files to dicom or tiff files](https://discourse.slicer.org/t/philips-epiq-7-vol-files-to-dicom-or-tiff-files/9602)
**Author:** [@deepz](https://discourse.slicer.org/u/deepz)\ **Replies:** 3\ **Last updated:** [December 30, 2019, 3:11pm UTC](https://discourse.slicer.org/t/philips-epiq-7-vol-files-to-dicom-or-tiff-files/9602 "2019-12-30T15:11:51Z")
Hello Everyone, I am trying to convert 3d/4d volume files of cardiac slices( from philips epiq7) to dicom or tiff files. In the converter option , the format is not recognized itself. Kindly share your input. --- ## [Whole bovine brain segmentation/registration](https://discourse.slicer.org/t/whole-bovine-brain-segmentation-registration/9662)
**Author:** [@DanTran](https://discourse.slicer.org/u/DanTran)\ **Replies:** 0\ **Last updated:** [December 30, 2019, 3:04pm UTC](https://discourse.slicer.org/t/whole-bovine-brain-segmentation-registration/9662 "2019-12-30T15:04:27Z")
Hi, I work on bovine brains and am trying to fully segment pre and postoperative MRIs, then register them to compute the difference in brain tissue between the two sets of MRIs. I have put plastic fiducials to help with… --- ## [Importing slicer libraries separately, outside embedded Python, like in Conda or Jupiter environments](https://discourse.slicer.org/t/importing-slicer-libraries-separately-outside-embedded-python-like-in-conda-or-jupiter-environments/9645)
**Author:** [@Jason\_West](https://discourse.slicer.org/u/Jason_West)\ **Replies:** 1\ **Last updated:** [December 29, 2019, 7:10pm UTC](https://discourse.slicer.org/t/importing-slicer-libraries-separately-outside-embedded-python-like-in-conda-or-jupiter-environments/9645 "2019-12-29T19:10:14Z")
Hey Everyone, I was curious if anyone here has had success using the slicer libraries importing from an outside Python, perhaps a lightweight build using swig to give access to all the libraries available in “import sli… --- ## [Problem in loading dicom ("Could NOT load image as Scalar Volume")](https://discourse.slicer.org/t/problem-in-loading-dicom-could-not-load-image-as-scalar-volume/9634)
**Author:** [@sam\_javidi](https://discourse.slicer.org/u/sam_javidi)\ **Replies:** 4\ **Last updated:** [December 29, 2019, 4:11pm UTC](https://discourse.slicer.org/t/problem-in-loading-dicom-could-not-load-image-as-scalar-volume/9634 "2019-12-29T16:11:16Z")
Hi I have a problem with loading Dicom MR images. Images are ‘RGB’ (true color), it is not loaded because of an error “Could NOT load image as Scalar Volume”. I am wondering if anyone knows how to solve this issue. im… --- ## [DeepInfer issues](https://discourse.slicer.org/t/deepinfer-issues/9622)
**Author:** [@hherhold](https://discourse.slicer.org/u/hherhold)\ **Replies:** 4\ **Last updated:** [December 29, 2019, 2:17am UTC](https://discourse.slicer.org/t/deepinfer-issues/9622 "2019-12-29T02:17:34Z")
I’m trying out DeepInfer and having a few issues. This with a Dec 20 nightly version with a recently downloaded Deepinfer module and I’ve had to make some changes to get it to work at all - First issue was ‘import Queue’… --- ## [3D slicer hangs most times](https://discourse.slicer.org/t/3d-slicer-hangs-most-times/9639)
**Author:** [@Ramya\_C](https://discourse.slicer.org/u/Ramya_C)\ **Replies:** 0\ **Last updated:** [December 29, 2019, 1:51am UTC](https://discourse.slicer.org/t/3d-slicer-hangs-most-times/9639 "2019-12-29T01:51:59Z")
Operating system: Windows 10 Intel core I7 Slicer version: 4.8.1 Expected behavior: Actual behavior: I am using slicer 3D 4.8.1 version for modelling. However I am facing issue of hanging for every single event. Eve… --- ## [Limitation in increasing the resolution in Crop Volume module](https://discourse.slicer.org/t/limitation-in-increasing-the-resolution-in-crop-volume-module/9621)
**Author:** [@Tekk\_ya](https://discourse.slicer.org/u/Tekk_ya)\ **Replies:** 1\ **Last updated:** [December 26, 2019, 4:11pm UTC](https://discourse.slicer.org/t/limitation-in-increasing-the-resolution-in-crop-volume-module/9621 "2019-12-26T16:11:01Z")
Operating system: Windows 10 Slicer version: 4.10.1 and 4.10.2 Hi all, I want to increase the resolution of CT scans in the crop volume module. I have cropped the original scan with my selected ROI and I haven’t appli… --- ## [Segmentation of tumor in CT image using contour points of RT Struct](https://discourse.slicer.org/t/segmentation-of-tumor-in-ct-image-using-contour-points-of-rt-struct/1695)
**Author:** [@Apurva](https://discourse.slicer.org/u/Apurva)\ **Replies:** 4\ **Last updated:** [December 21, 2017, 4:38am UTC](https://discourse.slicer.org/t/segmentation-of-tumor-in-ct-image-using-contour-points-of-rt-struct/1695 "2017-12-21T04:38:00Z")
Hey, I am Apurva. I am currently pursuing my Masters at George Washington University. I am currently working on analysis of the effectiveness of Radiation Therapy for the treatment of patients suffering from Head and Ne… --- ## [Occlusion Registration](https://discourse.slicer.org/t/occlusion-registration/9614)
**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\ **Replies:** 2\ **Last updated:** [December 26, 2019, 9:56am UTC](https://discourse.slicer.org/t/occlusion-registration/9614 "2019-12-26T09:56:34Z")
Dear all, Is there way to achieve this with the 3D Slicer ? First makes scans of upper jaw and lower jaw and then export them as stls (because thats the only available option) Then is there a way to get them registere… --- ## [Heat maps for two structures](https://discourse.slicer.org/t/heat-maps-for-two-structures/9610)
**Author:** [@Jainey](https://discourse.slicer.org/u/Jainey)\ **Replies:** 3\ **Last updated:** [December 25, 2019, 6:30pm UTC](https://discourse.slicer.org/t/heat-maps-for-two-structures/9610 "2019-12-25T18:30:37Z")
Is there a module that I can create heat maps for two segmented structures please. I want to assess the proximity of the surfaces Thanks --- ## [Need help regarding porosity maps of tumor using 3-D slicer](https://discourse.slicer.org/t/need-help-regarding-porosity-maps-of-tumor-using-3-d-slicer/9609)
**Author:** [@Shahid\_Khan](https://discourse.slicer.org/u/Shahid_Khan)\ **Replies:** 0\ **Last updated:** [December 25, 2019, 4:22am UTC](https://discourse.slicer.org/t/need-help-regarding-porosity-maps-of-tumor-using-3-d-slicer/9609 "2019-12-25T04:22:33Z")
Hey, I am Shahid Khan and I have just started using 3-D slicer(a week ago) for my project. I am working on lung tumor. I have extracted DICOM CT data of lung cancer from TCIA. I need porosity(Ve) and permeability(Ktrans… --- ## [How to analyse CT time sequence data of lungs?](https://discourse.slicer.org/t/how-to-analyse-ct-time-sequence-data-of-lungs/9620)
**Author:** [@Shahid\_Khan](https://discourse.slicer.org/u/Shahid_Khan)\ **Replies:** 6\ **Last updated:** [December 28, 2019, 6:42am UTC](https://discourse.slicer.org/t/how-to-analyse-ct-time-sequence-data-of-lungs/9620 "2019-12-28T06:42:37Z")
Hey, I am Shahid Khan and I am very new to 3-d slicer(started a week ago). I want to analyze CT data of lung cancer and want to generate Ktrans and Ve maps. I have data in Scalar volume but to use T1 mapping I need it in… --- ## [Loading DICOM volume got significantly slower](https://discourse.slicer.org/t/loading-dicom-volume-got-significantly-slower/9605)
**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\ **Replies:** 2\ **Last updated:** [December 24, 2019, 6:09pm UTC](https://discourse.slicer.org/t/loading-dicom-volume-got-significantly-slower/9605 "2019-12-24T18:09:06Z")
Here are the logs when loading the same DICOM volume with the ‘Add data’ menu on Linux : On 2019-11-11 (don’t know the revision tag) : There is more than one file, use the vtkITKArchetypeImageSeriesReader instead Load… [Previous page](https://discourse.slicer.org/c/support/11.md?page=357) [Next page](https://discourse.slicer.org/c/support/11.md?page=359)