Lead-DBS
  • Home
  • About
    • Quickstart Primer (Post-OP MR-Scans)
    • Data & Code inclusion philosophy
    • Quickstart Primer (Post-OP CT-Scans)
    • Deep Brain Stimulation
    • Lead Connectome
    • Publications
    • List of Lead-DBS dependencies
    • Citing Lead-DBS
  • News
  • Contact
  • Help/Support
    • Manual
    • Knowledge Base
      • Atlases/Resources
        • Subcortical Atlases (MNI-Space)
        • Cortical Atlas Parcellations (MNI-Space)
        • Macaque Atlases (MNI-Space)
        • The DISTAL atlas
        • FEM-based VTA model
        • Normative Connectomes
      • Lead-DBS Methods
        • Subcortical Electrophysiology Mapping (SEM)
        • AC/PC to MNI conversion
        • Connectivity Benefit Mapping
      • Other Videos
      • Screenshots
      • Walkthrough-Videos
    • Slack User Channel
    • Forum
  • Workshops
    • Past workshops
      • Berlin 2016
      • Shanghai September 2018
      • Hamburg February 2019
    • Berlin September 2019
    • Machine Learning – Berlin September 2019
    • Brisbane February 2020
  • Download
  • Lead-Connectome
  • Search
  • Menu Menu

Issue with Import of Post-op CT DICOM Files

You are here: Home1 / Forums2 / Support forum ARCHIVED – Please use Slack Channel instead3 / Issue with Import of Post-op CT DICOM Files4

Tagged: DICOM Files, Import

Viewing 2 posts - 1 through 2 (of 2 total)
  • Author
    Posts
  • 07/01/2019 at 5:23 AM #7720
    Diaz0188
    Participant

    Hi,

    I am having difficulties with one of the DICOM files that I am trying to import into Lead DBS. When I ‘Run’ the import and rename functions it imports the T1 and T2 files but not the CT (“Ignoring derived image(s) of series 3”). Below is the output I get in Matlab with the error. I have run many files with Lead DBS and have never experienced this error:

    Importing DICOM files…
    Compression will be faster with ‘pigz’ installed http://macappstore.org/pigz/
    Chris Rorden’s dcm2niiX version v1.0.20190410 (JP2:OpenJPEG) (JP-LS:CharLS) Clang10.0.1 (64-bit MacOS)
    Found 380 DICOM file(s)
    Warning: interpolated protocol ‘t2_tse_tra’ may be unsuitable for dwidenoise/mrdegibbs. /Users/diazcomputer/Desktop/Anonymous Pt/DICOM/IMG-0005-00001.dcm
    Convert 180 DICOM as /Users/diazcomputer/Desktop/Anonymous Pt/DICOM_t1_fl3d_tra_iso_20170131130813_5 (208x256x180x1)
    Cropping from slice 8 to 177 (of 180)
    Ignoring derived image(s) of series 3 /Users/diazcomputer/Desktop/Anonymous Pt/DICOM/IMG-0001-00001.dcm
    Convert 90 DICOM as /Users/diazcomputer/Desktop/Anonymous Pt/DICOM_t2_tse_tra_20170131130813_6 (512x512x90x1)
    Conversion required 0.492053 seconds (0.476087 for core code).
    ** Process done.

    I can send you the anonymized DICOM files if you’d like.

    Thank you so much for your time and I hope to hear from you soon.

    Best,
    Diaz0188

    07/01/2019 at 5:46 AM #7721
    andreashorn
    Keymaster

    Hi hi,

    I fear we’re also no experts with dicom imports, best ask the question in the dcm2nii forums.
    I assume you have tried importing with all three methods already (dcm2niix, dicm2nii and SPM)?
    Most likely the DICOM file is corrupted.

    Best, Andy

  • Author
    Posts
Viewing 2 posts - 1 through 2 (of 2 total)
  • The forum ‘Support forum ARCHIVED – Please use Slack Channel instead’ is closed to new topics and replies.

Your Account

Log In
Register

Forum Statistics

Registered Users
131
Forums
1
Topics
185
Replies
607
Topic Tags
81

Subscribe to our newsletter

Latest Tweets

  • Tweet Avatar
    leaddbs
    @leaddbs
    RT @nastasiayendiki: 1/ Update from round 2 of the IronTract Challenge (for more, watch out for #ISMRM2021 talk by @chiaramff - with… https://t.co/Fgxg8kds4d

    2d
  • Tweet Avatar
    leaddbs
    @leaddbs
    RT @andreashorn_: I was very honored about the possibility to interview one of my true heroes in the field of DBS modeling in a new… https://t.co/GTtgDOwZBi

    4d
  • Tweet Avatar
    leaddbs
    @leaddbs
    RT @MGHNeuroSci: Mark Richardson, MD, PhD, director of Functional Neurosurgery at @mghneurosurg, discusses the successful use of dee… https://t.co/zyPXo98pvt

    4d

Recent Posts

  • Lead-DBS v2.5 out now!
  • Lead-DBS on the cover of NeuroImage
  • Lead-DBS on the cover of Biological Psychiatry
  • Lead-DBS on the cover of Annals of Neurology
  • Crucial methodological updates for Lead-DBS

Archives

  • March 2021
  • September 2020
  • June 2019
  • November 2018
  • September 2018
  • August 2018
  • March 2018
  • November 2017
  • September 2017
  • July 2017
  • April 2017
  • July 2016
  • June 2016
  • May 2016
  • March 2016
  • December 2015
  • November 2015
  • April 2015
  • January 2015
  • December 2014
  • October 2014
  • September 2014
  • July 2014
  • June 2014

Impressum & Datenschutzerklärung

Scroll to top