ImageStacks module won't load full tiff stack

Support
1

Operating system: Windows 11
Slicer version: 5.8.1
Expected behavior: importing a tiff stack with the slicermorph ImageStacks (3,867 images)
Actual behavior: only selects a subset of the stack

Hello,

I’m trying to import a tiff stack that I downloaded from morphosource - Making sure you're not a bot!

It’s a CT scan of a shark and when I load it into slicer, it’s missing the head. I have imported the stack into FIJI to verify the head is indeed captured in the image stack.

I unzipped the morphosource download and when I try to import it into 3DSlicer via ImageStacks, it only loads some of the stack–In the 2D views I can see everything except the head of the shark, it seems cut off. I’ve made sure to enter the spacing information from the morphosource page so I’m unsure what I"m doing wrong. In the ImageStacks module I tried selecting all the files manually rather than the “Browse” and selecting one file, and when I added them all manually the scan alignment became jagged.

I’m including screenshots of the stack in FIJI where the shark’s head is visible, and a screenshot of how it looks in slicer when I use the “browse” feature, and “select files”.

Any guidace would be super appreciated, I’m sure I’m missing something just not sure what. Thanks in advance!

Ctaurus stack in FIJI
Ctaurus stack in FIJI1295×323 94.4 KB

Ctaurus stack in Slicer using imagestacks browse
Ctaurus stack in Slicer using imagestacks browse1178×874 116 KB

Ctaurus stack in Slicer using imagestacks select all files
Ctaurus stack in Slicer using imagestacks select all files1188×873 83.2 KB

2

Please try with the latest stable, v5.10.0 (your Slicer is couple years old). It worked perfectly fine for me:

image
image1662×1208 271 KB

3

Hi Murat,

Thanks for your prompt reply. I downloaded slicer5.10 and am still having the same issue. I tried again by using the “browse” option of the ImageStacks module and it still won’t load the head. If I manually select all the files it still gets the jagged appearance (screenshots attached).

slicer5.10_screengrab_manualselectfiles
slicer5.10_screengrab_manualselectfiles1919×1004 374 KB

slicer5.10_screengrab
slicer5.10_screengrab1916×1002 231 KB

4

The one the top is right, there are 3867 slices in this sequence. The one in the bottom is incorrect, because it leaving out about 1000 slices for some reason.

If you select the files yourself, ImageStacks uses the sorting provided by the file system, which can be wrong (e.g., sorted by dates, filesize instead of the correct sequence) etc… I suggest clearing your scene (CTRL+W) and then dragging the very first file (Ctau_Highres_FullBody0000.tif) into the slicer, and then let slicer sort the files.

It should look something like this:

image

%04d means the sequences in filenames are expected to have four (4) numerical digits, which is the correct format for this.