[Top][All Lists]

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: dicom package does not recognize gdcm package (on which it is depend

From: Andy Buckle
Subject: Re: dicom package does not recognize gdcm package (on which it is dependend)
Date: Sat, 7 Mar 2015 14:31:13 +0000

On 5 March 2015 at 10:55, Lennart Geurts <address@hidden> wrote:
Dear all,

This is the first time I use this mailing list, I hope I dont use it inappropriately. I have searched previous questions and found a similar problem from a user on OSx. However I run a Debian (Jessie) distribution and Im not sure how alike these are. I am from the medical imaging community and at the office I use a windows environment with matlab. At home I started using a linux environment and want to use octave, for which the dicom package is essential (my data is in the dicom format and not readily converted to nifti because of its high dimensionality, it would require many,many seperate files).

The dicom package is dependend on the gdcm library, which I have installed. The when installing the dicom package I get this error:

fatal error: gdcm-2.0/gdcmReader.h: No such file

The current gdcm version is newer than 2.0 so I thought maybe I should use the older version, but the error remained. Even the older function did not get installed to that path. I think the dicom package does not look at which path it should use.

Maybe this is a bug because the path is hardcoded (as suggested in the similar OSx thread)
Maybe this happens because the last release is from 2011 and the package is just not maintained anymore, while gdcm keeps getting updates.
Maybe Im just doing something horribly wrong that Im not seeing.

If anybody has some hints/ideas that would help a lot thanks!


I recently got the dicom package working on
debian 7.8
octave 3.8.2
gdcm2.2 (package name libgdcm2-dev)
up-to date (unreleased) dicom package
"download snapshot" from here

Carne made some automake magic, that I think will fix your issue.

cd dicom/src

you will need to get the resulting oct files (and the dic file) in octave's


/* andy buckle */

On 7 March 2015 at 11:15, Lennart Geurts <address@hidden> wrote:
Hi guys thanks a lot for your help.

I did have libgdcm2-dev installed (libgdcm2-dev is already the newest version. apt-get told me)

it now catches at this:
checking for GDCM... CMake Error: Problem processing arguments. Aborting.
CMake Error: Problem processing arguments. Aborting.
checking gdcmSystem.h usability... no
checking gdcmSystem.h presence... no
checking for gdcmSystem.h... no
configure: error: Unable to find GDCM headers (do you have CMake installed?)

I do have cmake and automake installed.

The way apt finds gdcm and the way cmake finds gdcm must be different. Somewhere in configure I read
 --find-package "-DNAME=GDCM"
Maybe I should replace GDCM with libgdcm2-dev?

(please bottom post)

I made a Debian Jessie RC1 install. I installed Octave 3.8.2 (standard in the repo for Jessie).

libgdcm2-dev gives you gdcm 2.4 on Jessie, whereas I get gdcm 2.2 from the same package name on wheezy.

This should not be a huge problem, as I have got the dicom package working on openSuSE with gdcm 2.4. It's some tricky file location thing that's the problem. Maybe it's just defeating automake, I don't know. I have run out of time for the moment.

/* andy buckle */

reply via email to

[Prev in Thread] Current Thread [Next in Thread]