⚠

NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug.

The Fiji project now uses GitHub Issues for issue tracking.

Please file all new issues there.

Bug 691 - Modern Mode (IJ2) fails to load DICOM
Modern Mode (IJ2) fails to load DICOM
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: ImageJ2
unspecified
PC Windows
: P5 normal
Assigned To: ImageJ Developers Mailing List
Depends on:
Blocks:
 
Reported: 2014-01-07 09:15 CST by Conor Heeney
Modified: 2014-02-02 20:26 CST
2 users (show)

See Also:

Attachments
Screenshot (441.27 KB, image/png)
2014-01-07 09:15 CST, Conor Heeney
DICOM test file (1.50 MB, application/octet-stream)
2014-01-08 10:44 CST, Conor Heeney

Description Conor Heeney 2014-01-07 09:15:03 CST 
Created attachment 127
Screenshot

Using Fiji (1.48o) downloaded today (07Jan14) on 32bit JRE (1.6.0_24).

Modern mode either doesn't read the DICOM header correctly, or if it does, then it misreads the DICOM image data.

Switching back to legacy mode, and the image is read and rendered correctly.

See attached screenshot for example.
Comment 1 Mark Hiner 2014-01-08 09:16:05 CST 
Hi Conor. Thanks for reporting this issue. I'm guessing it's a bug in the DICOM format support of SCIFIO (https://github.com/scifio/scifio).

All DICOM datasets I have access to are being read properly (in both pure IJ2 & Fiji's modern mode). So would it be possible for you to attach your dataset to this bug report? Then I can reproduce it locally and have a fix out shortly.

Thanks!
Comment 2 Conor Heeney 2014-01-08 10:44:32 CST 
Created attachment 128
DICOM test file

created by Varian Medical Systems linear accelerator.
Comment 3 Conor Heeney 2014-01-08 10:46:38 CST 
Mark

I've attached the DICOM file which was used in the screenshots.

I've also taken the liberty of opening other DICOM files with IJ2 to see what happens.

It's able to open Siemens CT files, however it takes approximately twice as long as legacy mode.
Comment 4 Mark Hiner 2014-01-08 13:15:53 CST 
Conor, this should be fixed in SCIFIO as of this commit: https://github.com/scifio/scifio/commit/61527ff0303721b8946c8da2f375d5885810b4df

I'll try to cut a bug fix release and upload it to Fiji today or tomorrow.
Comment 5 Mark Hiner 2014-01-10 11:42:44 CST 
Uploaded SCIFIO 0.8.2 to Fiji. Looks like this dataset opens properly now in modern mode.
Comment 6 Alexa 2014-02-02 20:26:28 CST 
*** nothing to be seen here ***