Diogo Posted May 2, 2017 Share Posted May 2, 2017 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 Link to comment Share on other sites More sharing options...
mikefazz Posted May 3, 2017 Share Posted May 3, 2017 I haven't tried importing tiff's but one thing to try would be to use ImageJ to convert a stack of tiffs to an nrrd file for loading in 3DSlicer. Mike (not Dr. Mike;) Link to comment Share on other sites More sharing options...
Dr. Mike Posted May 3, 2017 Share Posted May 3, 2017 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 Link to comment Share on other sites More sharing options...
Terrie S Posted June 10, 2017 Share Posted June 10, 2017 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. Link to comment Share on other sites More sharing options...
Dr. Mike Posted June 21, 2017 Share Posted June 21, 2017 Amazing how the freeware (3D Slicer) works better than the expensive proprietary software (Mimics), at least for this application. Link to comment Share on other sites More sharing options...
Terrie S Posted June 29, 2017 Share Posted June 29, 2017 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! Link to comment Share on other sites More sharing options...
Diogo Posted October 5, 2017 Author Share Posted October 5, 2017 Sorry guys been so busy and only now could come back and read your responses. I ended up with Mevislab for segmentation and analysis. Here is an example of what I have been doing. Cheers. Diogo Guerreiro S18T7 Final.mp4 Link to comment Share on other sites More sharing options...
Dr. Mike Posted October 7, 2017 Share Posted October 7, 2017 Wow! Thanks for sharing. That is incredible detail! Link to comment Share on other sites More sharing options...
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