Visible human project MRI dataset loading

Operating system:Mac
Slicer version:4.10.2
Expected behavior: Trying to load dataset from Visible human project
Actual behavior: Loading problems

Hi - can you be more specific about which data you were trying to load and the problems were?

Hi sorry, I’m quite new to all this an wasn’t sure where to describe the problem in detail.

I downloaded the open source VHP datasets and have mainly been working with the 4K tiff images which load into Slicer with no serious problems (despite there being no header info)and have managed to make segmentations and 3D print them.

Now I am trying to load in the MRI data. The files come in 2 directorys, MRI images and then a separate directory of MRI headers which are text files.

The MRI images have a format that my mac is interpreting as a zip file I think but when I try to open it I just get an exec file

If I drag and drop this directory into 3Dslicer, nothing happens, and it also won’t load it into the DICOM database, presumably because the header files are in a separate directory.

My next plan is to separate the images into their individual series… t1, t2 etc and see if that works, but a link to a tutorial or any suggestions would be much appreciated.

I am very much a beginner at all this so am struggling a little bit with the language of this software. please excuse my naive questions.

Thanks

Amy

The visible human data is not in DICOM format. It is distributes with “Z” compression, in the GE Signa format. This format was proprietary and pre-dates DICOM.

You can convert this format to NIfTI with the following steps

  • Uncompress all of the images. From the command line, this would be uncompress *.Z
  • Convert the images to NIfTI using dcm2nii (which pre-dates dcm2niix). This software was distributed with MRIcron - just get the 2016 version or earlier. The only benefit of this old software relative to dcm2niix is support for these archival proprietary formats. Be aware that the Signal format does not include much information about image spacing and orientation. Therefore, you may have to tune the resulting NIfTI header by hand.

The visible human scans are very old, and you should keep your expectations realistic. While the color photographs (particularly for the female) are unique, the MRI and CT scans are obsolete. Pressing the “Download Sample Data” button in Slicer will provide you access to far better MRI and CT images.

Chris,
Thank you sooo much for your super helpful reply. I didn’t realise that MRI and CT data formats had changed so much. I will definitely check out the sample data as you suggested and if I can’t find any of the areas I need, I’ll try converting the old dataset. I’ll post a link to my project here when/if I have something interesting to show :wink:

What anatomy are you interested in?

I’m interested in looking at the negative spaces of our bodies and organs. The cavities within and ‘packing fascia’ between organs.
I still haven’t managed to locate a free online dataset of the thorax that is good enough quality so if you know of any I’d be super grateful for a pointer.

Cheers

Amy

There are a lot of very good scans on TCIA. Even though the folks are ill with cancer, much of rest of the anatomy is well represented.

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