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Diogo

Teeth Micro CT

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Dear all

 

First of all thank you so much Dr Mike for this wonderful website.

I am with the University of Michigan and been doing some research on teeth morphology using Micro CTs.

I am working mostly with MeVislab frameworks and Mimics.

Regarding slicer I would like to ask if it is possible to import TIFF files as slices instead of DICOM files.

Each time I try to import data in TIFF my slicer version keeps crashing.

Any tips?

 

Best Regards

 

Diogo

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I think it is possible to import a stack of TIFF or JPG files in Slicer using the Add data feature. Once the images are imported you will need to tell Slicer how far apart they are spaced, since unlike a DICOM series, individual TIFF files have no information about slice spacing. I haven't tried this personally, but here is a link

 

mikefazz is correct about ImageJ, and its derivative, Fiji. I have had some trouble with the left-right and cranial-caudad orientation of the file getting mixed up with Fiji which required me to import the data into Slicer anyway to do a mirror transform. Maybe you will have better luck.

 

If you are creating dental files using Mimics I would suggest you also give the democratiz3D service on this site a try. Once you load your file into Slicer you can export it into NRRD format (anonymized) and upload it to democratiz3D. Conversion to STL takes about 15 minutes and it is scalable, meaning you can upload multiple files and it will process them all concurrently. As of March 20, 2017 there is improved support specifically for dental CT files (see version history here).  The main reason to use the automated democratiz3D is that it saves time over Mimics and can do batch processing of multiple jobs simultaneoulsy. Also, it is free compared to thousands of $$$ for Mimics, but since you already have a Mimics license that may not be important to you. 

 

On another note, I am planning on doing a dental scan specific tutorial soon. Look for that in the coming weeks.

 

Good luck!

 

Dr. Mike

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Hi Diogo,

 

I have started working with microCT and can't get them in to Mimics. However, I have had great success with 3DSlicer. It's very slow with the tiff stack, but if I import the tiff stack to Fiji and save it as a .nrrd file, then Slicer reads it much faster.

 

Terrie

P.S. What version of Mimics are you using? I have 17 and 18 and they both seem to have a hard time with tiff stacks.

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I know! I just figured out how to create a dicom series in Slicer from the nrrd file. Mimics can read the dicom series, but I had to use Slicer to create the orthogonal views because that's where Mimics was getting hung up for me!

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