Trouble with opening a DICOM file from Siemens Vida


#1

Hello,

I have trouble working with images from Siemens Vida. I heard that there is some special new format in use, as I looked at the file it also contains some xml (although it is a DICOM file). Does anyone have experience with this?

mrinfo file gives me

mrinfo: [ERROR] unknown format for image file
mrinfo: [ERROR] error opening image

I can share the file per E-mail.

Thanks,

Amir


#2

Hi @amirzolal,

Happy to take a look, feel free to send me the file directly (jdtournier@gmail.com).
Cheers,
Donald.


#3

Sent per E-mail. Thanks alot!


#4

OK, I’ve had a look at the file, and it opens up straight away in mrinfo or mrview:

$ mrinfo  10000539/
mrinfo: [done] scanning DICOM folder "10000539/"
mrinfo: [100%] reading DICOM series ""
mrinfo: [WARNING] slice gap detected (maximum gap: 0.000193mm)
mrinfo: [WARNING] slice separation is not constant (from 1.9998653 to 2.0001934mm)
************************************************
Image:               "Anonymous Patient  [MR]"
************************************************
  Dimensions:        110 x 110 x 20 x 31
  Voxel size:        2 x 2 x 2 x ?
  Data strides:      [ -1 -2 3 4 ]
  Format:            DICOM
  Data type:         unsigned 16 bit integer (little endian)
  Intensity scaling: offset = 0, multiplier = 1
  Transform:               0.9998     0.01885   -0.002852      -102.2
                         -0.01768      0.9728      0.2308      -107.7
                         0.007124     -0.2307       0.973      -26.05
  EchoTime:          0.062
  comments:          Anonymous Patient  [MR]
                     DOS: 03/04/2018 21:33:32

What was the problem exactly? Maybe you’re running very old version? What does mrinfo -version report?


#5

Oh … not that old at all … i ran mrinfo on the first file in the directory thinking it would read the whole series. When I run it on the directory everything is ok.

Sorry. Me stupid.

A.

== mrinfo 3.0_RC2-117-gf098f097 ==
64 bit release version, built Feb 6 2018, using Eigen 3.2.5
Author(s): J-Donald Tournier (d.tournier@brain.org.au) and Robert E. Smith (robert.smith@florey.edu.au)
Copyright © 2008-2017 the MRtrix3 contributors.

This Source Code Form is subject to the terms of the Mozilla Public
License, v. 2.0. If a copy of the MPL was not distributed with this
file, you can obtain one at http://mozilla.org/MPL/2.0/.

MRtrix is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty
of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

For more details, see http://www.mrtrix.org/.


#6

All good! Glad to hear it. :+1: