# Beginner Questions **URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=26 [Latest](https://discourse.itk.org/latest.md) · [Categories](https://discourse.itk.org/categories.md) · [Tags](https://discourse.itk.org/tags.md) **Page:** 27 --- ## [itk-vtkglue swig error](https://discourse.itk.org/t/itk-vtkglue-swig-error/3309)
**Author:** [@SiPyWiFi](https://discourse.itk.org/u/SiPyWiFi)\ **Replies:** 2\ **Last updated:** [July 22, 2020, 5:54am UTC](https://discourse.itk.org/t/itk-vtkglue-swig-error/3309 "2020-07-22T05:54:47Z")
Hi, If i import the itk.ImageToVTKFilter(), I get the error: AttributeError: module 'itk.ITKVtkGluePython' has no attribute 'swig' I am using: itk==5.1.0.post3 vtk==8.1.2 itk-vtkglue==0.3.0 How can i solve this er… --- ## [Registering with Rigid and a tiny bit of Affine transform](https://discourse.itk.org/t/registering-with-rigid-and-a-tiny-bit-of-affine-transform/3311)
**Author:** [@nvladimus](https://discourse.itk.org/u/nvladimus)\ **Replies:** 4\ **Last updated:** [July 21, 2020, 9:26pm UTC](https://discourse.itk.org/t/registering-with-rigid-and-a-tiny-bit-of-affine-transform/3311 "2020-07-21T21:26:17Z")
Hi, everyone, My first post here, please be merciful. I am using simpleITK for 3D microscopy image registration, and it generally works well for rigid transformations. My moving image is a bit skewed, so I’d like to add… --- ## [Problem in extracting mnc file](https://discourse.itk.org/t/problem-in-extracting-mnc-file/3316)
**Author:** [@Alsurayhi](https://discourse.itk.org/u/Alsurayhi)\ **Replies:** 2\ **Last updated:** [July 21, 2020, 7:50pm UTC](https://discourse.itk.org/t/problem-in-extracting-mnc-file/3316 "2020-07-21T19:50:24Z")
Hi all, I am using the following code in order to convert MNC file to readable format for 3D slicer. But there are some errors in the code. for example in line 52 , it is mentioning qualified name is not allowed. I downl… --- ## [Example vector images](https://discourse.itk.org/t/example-vector-images/3314)
**Author:** [@bhb2048](https://discourse.itk.org/u/bhb2048)\ **Replies:** 2\ **Last updated:** [July 21, 2020, 7:13pm UTC](https://discourse.itk.org/t/example-vector-images/3314 "2020-07-21T19:13:15Z")
In Examples/Data, which images are vector images? Thanks Barry --- ## [(Just) isotropic scaling](https://discourse.itk.org/t/just-isotropic-scaling/3306)
**Author:** [@david.russell](https://discourse.itk.org/u/david.russell)\ **Replies:** 3\ **Last updated:** [July 21, 2020, 1:36pm UTC](https://discourse.itk.org/t/just-isotropic-scaling/3306 "2020-07-21T13:36:54Z")
I’m trying to do registration in 2D using only one scale parameter applied to to both axes. I believe this is called isotropic scaling. I’ve been struggling because the scale transform is ansiotropic. I was thinking that… --- ## [how to use ReadImageDICOMFileSeries on a zipfile](https://discourse.itk.org/t/how-to-use-readimagedicomfileseries-on-a-zipfile/3277)
**Author:** [@lonewolf](https://discourse.itk.org/u/lonewolf)\ **Replies:** 7\ **Last updated:** [July 20, 2020, 3:55pm UTC](https://discourse.itk.org/t/how-to-use-readimagedicomfileseries-on-a-zipfile/3277 "2020-07-20T15:55:53Z")
Hi all, I am trying to unzip a file with CT series in it and I can only display one image. When I try passing multiple images, it fails. I am using itk.js 13.1.1. This is the error: message: “FS error” stack: “\ **Author:** [@blizzardboi\_2020](https://discourse.itk.org/u/blizzardboi_2020)\ **Replies:** 2\ **Last updated:** [July 20, 2020, 3:28am UTC](https://discourse.itk.org/t/cropping-a-ct-volume/3302 "2020-07-20T03:28:24Z") Hello. I want to crop(28x28x50) all the dcm (CT) volumes(150x150x50) in a folder, any python script for that? --- ## [Within-subject registration of an MRI image acquired at 1.5 Tesla to another image acquired at 3 Tesla](https://discourse.itk.org/t/within-subject-registration-of-an-mri-image-acquired-at-1-5-tesla-to-another-image-acquired-at-3-tesla/3299)
**Author:** [@MSherafati74](https://discourse.itk.org/u/MSherafati74)\ **Replies:** 2\ **Last updated:** [July 18, 2020, 10:13pm UTC](https://discourse.itk.org/t/within-subject-registration-of-an-mri-image-acquired-at-1-5-tesla-to-another-image-acquired-at-3-tesla/3299 "2020-07-18T22:13:08Z")
Hello, I have a presumably elementary registration task at hand. I am familiar with Python and have just learned the basics of the registration concept from some online resources. I intend to tackle the job using SimpleI… --- ## [Working with large field medical images](https://discourse.itk.org/t/working-with-large-field-medical-images/3238)
**Author:** [@juccapirama](https://discourse.itk.org/u/juccapirama)\ **Replies:** 8\ **Last updated:** [July 17, 2020, 11:51am UTC](https://discourse.itk.org/t/working-with-large-field-medical-images/3238 "2020-07-17T11:51:00Z")
Hello, I’m working on a preprocessing and a segmentation pipeline for vessel extraction from micro-scan medical images. The image volumes are around 2048x2048x1400 and 2560x2560x1400, with 5,5 Gb and 8,5 Gb in 8 bits. I… --- ## [reading dynamic or gated SPECT images](https://discourse.itk.org/t/reading-dynamic-or-gated-spect-images/3283)
**Author:** [@KrisThielemans](https://discourse.itk.org/u/KrisThielemans)\ **Replies:** 1\ **Last updated:** [July 14, 2020, 7:45pm UTC](https://discourse.itk.org/t/reading-dynamic-or-gated-spect-images/3283 "2020-07-14T19:45:37Z")
I need to read SPECT dynamic or gated images in DICOM format. In contrast to MR CT and PET where the data is spread over multiples files (with for each 2D slice), SPECT images are usually stored in a single file. For si… --- ## [python code for DiffeomorphicDemonsRegistration in SimpleITK](https://discourse.itk.org/t/python-code-for-diffeomorphicdemonsregistration-in-simpleitk/1937)
**Author:** [@EE18D504\_SINDHURA\_C](https://discourse.itk.org/u/EE18D504_SINDHURA_C)\ **Replies:** 6\ **Last updated:** [July 14, 2020, 1:36pm UTC](https://discourse.itk.org/t/python-code-for-diffeomorphicdemonsregistration-in-simpleitk/1937 "2020-07-14T13:36:26Z")
I used a few methods for registration. Simple ITK in python looks very easy than using c++ for me. Is there any python code available for DiffeomorphicDemonsRegistration? --- ## [Convert volume from voxels to mm^3 or cm^3](https://discourse.itk.org/t/convert-volume-from-voxels-to-mm-3-or-cm-3/3280)
**Author:** [@agatadefr](https://discourse.itk.org/u/agatadefr)\ **Replies:** 3\ **Last updated:** [July 13, 2020, 1:47pm UTC](https://discourse.itk.org/t/convert-volume-from-voxels-to-mm-3-or-cm-3/3280 "2020-07-13T13:47:32Z")
Hey Guys, I am quite new in ITK. I implemented using LabelGeometryImageFilter. I extracted label volumes. Output results are in voxels. I would like to convert to cc\`3 or mm^3. Could you help me how I can do that ? … --- ## [AddObserver on DataObject](https://discourse.itk.org/t/addobserver-on-dataobject/3275)
**Author:** [@Come](https://discourse.itk.org/u/Come)\ **Replies:** 3\ **Last updated:** [July 10, 2020, 5:51pm UTC](https://discourse.itk.org/t/addobserver-on-dataobject/3275 "2020-07-10T17:51:49Z")
Hi, I want to add an observer to an image to know when it is modified. I tried the code below based on this example. #include \ #include \ #include \ class MyCommand : pu… --- ## [Create image patches and reconstruct it back to the image](https://discourse.itk.org/t/create-image-patches-and-reconstruct-it-back-to-the-image/3274)
**Author:** [@DL\_Begin](https://discourse.itk.org/u/DL_Begin)\ **Replies:** 6\ **Last updated:** [July 10, 2020, 12:54pm UTC](https://discourse.itk.org/t/create-image-patches-and-reconstruct-it-back-to-the-image/3274 "2020-07-10T12:54:28Z")
Hello, I have 3D medical image of size \[284,143,143\] , 284 are the number of slices and I want to extract 2D image patches out of it and reconstruct the image back to patches. I want to have patches of shape 128\*128 .I… --- ## [ITK octree](https://discourse.itk.org/t/itk-octree/3185)
**Author:** [@rolof](https://discourse.itk.org/u/rolof)\ **Replies:** 7\ **Last updated:** [July 9, 2020, 1:16am UTC](https://discourse.itk.org/t/itk-octree/3185 "2020-07-09T01:16:42Z")
Hi, I am trying to use Octrees on ITK, I saw that ITK have an Octree object. However, I can not find the methods of Octree to get the closest points. My problem is that I have a region of interest composed of several vo… --- ## [Update two dependent itk::DataObject](https://discourse.itk.org/t/update-two-dependent-itk-dataobject/3269)
**Author:** [@Come](https://discourse.itk.org/u/Come)\ **Replies:** 3\ **Last updated:** [July 7, 2020, 2:21pm UTC](https://discourse.itk.org/t/update-two-dependent-itk-dataobject/3269 "2020-07-07T14:21:22Z")
Hi, I created two itk::DataObject that are dependent and I would like to update both of them when any of the two is modified. I wonder if there is an easy way to do that (i.e. send a notification, from a DataObject, to … --- ## [Edit mask shape (add/remove pixels) using sitk](https://discourse.itk.org/t/edit-mask-shape-add-remove-pixels-using-sitk/3245)
**Author:** [@3omarkamal](https://discourse.itk.org/u/3omarkamal)\ **Replies:** 2\ **Last updated:** [July 2, 2020, 11:24am UTC](https://discourse.itk.org/t/edit-mask-shape-add-remove-pixels-using-sitk/3245 "2020-07-02T11:24:08Z")
I have multiple image sets with manually drawn masks (using ITK snap) and I want to edit the shape of the masks using simpleITK. For example, I tried sitk.BinaryDilate(label,1) to grow the regions by one pixel at the bou… --- ## [How to handle duplicte DICOM slices using SimpleITK?](https://discourse.itk.org/t/how-to-handle-duplicte-dicom-slices-using-simpleitk/3224)
**Author:** [@mattwarkentin](https://discourse.itk.org/u/mattwarkentin)\ **Replies:** 12\ **Last updated:** [June 29, 2020, 4:10pm UTC](https://discourse.itk.org/t/how-to-handle-duplicte-dicom-slices-using-simpleitk/3224 "2020-06-29T16:10:46Z")
Hi, This isn’t strictly a SimpleITK issue, but I am wondering how to handle such an issue using SimpleITK. I have been given axial CT from a colleague (stored in DICOM format), and it contains 146 slices of dimension 51… --- ## [Creating a coefficient image from mask](https://discourse.itk.org/t/creating-a-coefficient-image-from-mask/3236)
**Author:** [@Michael\_Ef](https://discourse.itk.org/u/Michael_Ef)\ **Replies:** 2\ **Last updated:** [June 29, 2020, 1:22pm UTC](https://discourse.itk.org/t/creating-a-coefficient-image-from-mask/3236 "2020-06-29T13:22:32Z")
Hi all, what is the best way to create a coefficient image (in mhd format) with values between 0 and 1 from a segmented image (grayscale)? E.g. every pixel on the reference image with value 100 will hold the value 0.4 i… --- ## [Unable to use Fiji/ImageJ](https://discourse.itk.org/t/unable-to-use-fiji-imagej/3231)
**Author:** [@ChocoLite](https://discourse.itk.org/u/ChocoLite)\ **Replies:** 1\ **Last updated:** [June 26, 2020, 12:47pm UTC](https://discourse.itk.org/t/unable-to-use-fiji-imagej/3231 "2020-06-26T12:47:38Z")
Hi, I am trying to run setup.ipynb from the ISBI '20 tutorial on my computer. But, I’m getting the following error. I have installed Fiji Viewer on Ubuntu. The Fiji.app folder in my home directory (~/Fiji.app). I’m ve… --- ## [Read ROIs from Dicom file and convert to pixel index](https://discourse.itk.org/t/read-rois-from-dicom-file-and-convert-to-pixel-index/3223)
**Author:** [@malteekj](https://discourse.itk.org/u/malteekj)\ **Replies:** 4\ **Last updated:** [June 25, 2020, 1:20pm UTC](https://discourse.itk.org/t/read-rois-from-dicom-file-and-convert-to-pixel-index/3223 "2020-06-25T13:20:58Z")
I’m trying to extract ROIs from Dicom files and convert the coordinates from mm in the patient coordinate system to a pixel indexes on the CT 3D array. The ROIs are saved in their own dicom files, and were drawn on the C… --- ## [Struggling to do simple 3D rigid registration](https://discourse.itk.org/t/struggling-to-do-simple-3d-rigid-registration/3217)
**Author:** [@msb](https://discourse.itk.org/u/msb)\ **Replies:** 4\ **Last updated:** [June 24, 2020, 11:54pm UTC](https://discourse.itk.org/t/struggling-to-do-simple-3d-rigid-registration/3217 "2020-06-24T23:54:14Z")
Hello, I’m am struggling to perform a simple 3D rigid registration between 2 images. I have started with one of the tutorials, and tried to adapt it to my situation. Particularly I want to adjust it to do a rigid regist… --- ## [GPU memory leakage for GPUDemonsRegistrationFilter](https://discourse.itk.org/t/gpu-memory-leakage-for-gpudemonsregistrationfilter/3129)
**Author:** [@qiang-zhang-neu](https://discourse.itk.org/u/qiang-zhang-neu)\ **Replies:** 9\ **Last updated:** [June 22, 2020, 5:34am UTC](https://discourse.itk.org/t/gpu-memory-leakage-for-gpudemonsregistrationfilter/3129 "2020-06-22T05:34:44Z")
I need to use GPUDemonsRegistrationFilter in my project. However, I find it would cause gpu memory leakage. This problem can be repeated by the following code: #include "itkGPUDemonsRegistrationFilter.h" #include "itkHi… --- ## [Difference between ShrinkFactorPerLevel and Shrink](https://discourse.itk.org/t/difference-between-shrinkfactorperlevel-and-shrink/3189)
**Author:** [@reox](https://discourse.itk.org/u/reox)\ **Replies:** 3\ **Last updated:** [June 19, 2020, 1:09pm UTC](https://discourse.itk.org/t/difference-between-shrinkfactorperlevel-and-shrink/3189 "2020-06-19T13:09:06Z")
I want to register some images, however the image size is too fine for my purposes and lower resolutions do need less memory and registration time. Resizing them to a 10th of the size should also work. I tried now two d… --- ## [Update image with itkwidget view 3D data](https://discourse.itk.org/t/update-image-with-itkwidget-view-3d-data/3202)
**Author:** [@emilljungberg](https://discourse.itk.org/u/emilljungberg)\ **Replies:** 3\ **Last updated:** [June 19, 2020, 12:44am UTC](https://discourse.itk.org/t/update-image-with-itkwidget-view-3d-data/3202 "2020-06-19T00:44:47Z")
Hi! I’ve recently started using the Python bindings for the latest version of ITK and it is working really great so far! I’m currently building an interactive application for testing effects of different filters with m… --- ## [How to get Statistics data in a region with non zero values](https://discourse.itk.org/t/how-to-get-statistics-data-in-a-region-with-non-zero-values/3200)
**Author:** [@Hasna\_R](https://discourse.itk.org/u/Hasna_R)\ **Replies:** 5\ **Last updated:** [June 18, 2020, 12:30pm UTC](https://discourse.itk.org/t/how-to-get-statistics-data-in-a-region-with-non-zero-values/3200 "2020-06-18T12:30:15Z")
I have a 3D label object collection.From that I need to find min max and mean value in another volume of same dimension. For that i took bounding box from label object and extracted the region from volume and used itk … --- ## [itk & using them in CLI/C++ wrapper projects](https://discourse.itk.org/t/itk-using-them-in-cli-c-wrapper-projects/3198)
**Author:** [@sag](https://discourse.itk.org/u/sag)\ **Replies:** 0\ **Last updated:** [June 17, 2020, 3:36pm UTC](https://discourse.itk.org/t/itk-using-them-in-cli-c-wrapper-projects/3198 "2020-06-17T15:36:09Z")
Hi all, I am trying to use c++/cli wrapper application to wrap around the c++ classes of ITK in order to call them from c# applications. I see simpleitk wrappers for the c# missing different classes so I want to build … --- ## [Problem in getting displacement field](https://discourse.itk.org/t/problem-in-getting-displacement-field/3127)
**Author:** [@basal](https://discourse.itk.org/u/basal)\ **Replies:** 1\ **Last updated:** [June 17, 2020, 10:14am UTC](https://discourse.itk.org/t/problem-in-getting-displacement-field/3127 "2020-06-17T10:14:49Z")
Hi, I used landmark warping code for deforming two sets of landmarks. The output is desirable and I wanted to get displacement field from the code. So I added the following part to the code but the displacement field is … --- ## [How to use Image filter on series images](https://discourse.itk.org/t/how-to-use-image-filter-on-series-images/3184)
**Author:** [@Amnesie](https://discourse.itk.org/u/Amnesie)\ **Replies:** 2\ **Last updated:** [June 16, 2020, 1:16pm UTC](https://discourse.itk.org/t/how-to-use-image-filter-on-series-images/3184 "2020-06-16T13:16:31Z")
Hallo everyone All example i can found about Morphological Image filter are base on single image. I tried some of them it can work on single image of my dataset. But, Now i import a dicom series and i want to do the sa… --- ## [error "Deprecated. Use equivalent C++11 header instead. see: vxl/scripts/UseStandardHeaders.py"](https://discourse.itk.org/t/error-deprecated-use-equivalent-c-11-header-instead-see-vxl-scripts-usestandardheaders-py/3167)
**Author:** [@zhaowg](https://discourse.itk.org/u/zhaowg)\ **Replies:** 4\ **Last updated:** [June 16, 2020, 2:41am UTC](https://discourse.itk.org/t/error-deprecated-use-equivalent-c-11-header-instead-see-vxl-scripts-usestandardheaders-py/3167 "2020-06-16T02:41:28Z")
Hi, Error info: fatal error C1189: #error: “Deprecated. Use equivalent C++11 header instead. see: vxl/scripts/UseStandardHeaders.py” ITK Version: 5.0.1 CMake Version： 3.17 My visual studio project was upgraded fro… [Previous page](https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=25) [Next page](https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=27)