turn a stack of png files into 3D image?

[cpinter (Csaba Pinter)]

I did a quick search on the forum. Let us know of none of these topics give you an answer

Unable to do 3D rendering from a sequence of tiff images

Operating system: linux ubuntu16 64bits Slicer version: 4.8.0 Expected behavior: load and render volume from 20 slices (gray scale) tiff images file Actual behavior: able to load file, appear in the Red windows only, no volume rendering.

Convert single files into one .nii

Hi, I have multiple single .ima files. These contain single slices info. What I want to achieve is to merge all these into one .nii file. What is the best way to do that? Thanks

Orienting .tiff images in axial/sagittal planes

I have two stacks of .png images, imported as .tiff files, corresponding to axial and sagittal MRI data. Once I put them into Slicer using the “Data” panel, both stacks are only visible using the “Axial” view. I am trying to segment a 3D volume using the segmentation editor, but since the views are both marked as Axial, the paint tool for each volume is not aligned. I have tried using transforms to switch the plane of the Sagittal .tiff image stack, but it only flips the data in the axial view. …

How to create 3D from 2D slices?

Operating system: MacOS Slicer version:4.11.20210226 Expected behavior: Actual behavior: I want to reconstruct 10 2D images to 3D. I have tried MatLab but I am having difficulties interpolating the gaps in between the adjacent slices. A colleague told me to try Slicer but I don’t know how to navigate the app. Here is the link to the slices:Dropbox - OCT_42_pix - Simplify your life I want to recreate a solid 3D. Thanks

Loading a .bmp sequence from directory as a LabelMap

Operating system: Windows 10 Education Slicer version: 5.0.2 Expected behavior: I have a set of segmented slices in a directory. It has 2 classes (0 and 255). The image format is .bmp. I want to load them as a segmentation. Actual behavior: I was following the official docs. However, when I load as a volume and select LabelMap it gives the following error. UpdateFromSeries: Unsupported number of components: 1 != 3 vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal: Cannot read file as a …

Calculating volumes from image stacks, scale does not match up.

Im working on a project where i need to determine the volume of fibrosis in cochlea’s. the raw data consists of +/- 100 microscopic photo’s of the cut up cochlea that i aligned and stacked in order(.tiff file). I coloured the segments ( bone; internal space; fibrosis) and tried to use segment statistics to find the volumes of the different segments. when i did this however i got volumes in the thousands cm3. The size differences between the segments seem right but the scale is not. Can i fix th…