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IDProjectCategoryView StatusLast Update
0003053Slicer4Module BRAINSpublic2014-09-17 22:57
Reporterpohl Assigned Tojcfr  
PrioritynormalSeveritymajorReproducibilityalways
Status closedResolutionfixed 
PlatformLinuxOSUbuntu 64 bitOS Version12.04
Product Version 
Target VersionSlicer 4.4.0Fixed in VersionSlicer 4.4.0 
Summary0003053: Brainsfit does not compile when compiling DICOM without Slicer
Description

cd superbuild

set Slicer_BUILD_DICOM_SUPPORT to off

make

/software/Slicer4/superbuild-nodicom/BRAINSTools/DWIConvert/DWIConvert.cxx:32:37: fatal error: itkDCMTKSeriesFileNames.h: No such file or directory

make[5]: [Modules/CLI/BRAINSTools/DWIConvert/CMakeFiles/DWIConvert.dir/DWIConvert.cxx.o] Error 1
make[4]:
[Modules/CLI/BRAINSTools/DWIConvert/CMakeFiles/DWIConvert.dir/all] Error 2
make[4]: Waiting for unfinished jobs....
[ 20%] Built target BRAINSLandmarkInitializer
[ 20%] Built target BRAINSROIAuto
[ 20%] Built target BRAINSSnapShotWriter
make[3]:
[all] Error 2
make[2]: [Slicer-prefix/src/Slicer-stamp/Slicer-build] Error 2
make[1]:
[CMakeFiles/Slicer.dir/all] Error 2
make: *** [all] Error 2

compilation terminated.

TagsNo tags attached.

Activities

2013-04-05 07:33

 

blub.log (250,507 bytes)
hjmjohnson

hjmjohnson

2014-01-06 16:15

developer   ~0010482

Steve,

We have discussed that turning off DICOM support in slicer is really not a good option any longer due to it's pervasive and important roll.

I would be more willing to remove the "Slicer_BUILD_DICOM_SUPPORT" than to support the an infrastructure both with and without it.

I'm willing to take on the challenge of removing "Slicer_BUILD_DICOM_SUPPORT" if you want to assign that to me.

Hans

pieper

pieper

2014-01-07 02:48

administrator   ~0010484

I agree Hans - let's touch base with Jc today on this. We had a similar discussion a year or so ago when I added a dicomDatabase member to the slicer application because I think dicom is core to most slicer use cases. I don't want to encourage the style of medical imaging research that pretends you can ignore dicom :)

pieper

pieper

2014-02-04 10:20

administrator   ~0010559

Reminder sent to: jcfr

@Jc - what do you think of removing the option to build slicer without DICOM?

Alternatively, maybe we should make the BRAINS build be dependent on DICOM being enabled. This is probably more consistent with our current architecture.

jcfr

jcfr

2014-02-05 12:14

administrator   ~0010561

By doing a clean build with the option "Slicer_BUILD_DICOM_SUPPORT", the reported error won't occur. See [1]

[1] https://github.com/Slicer/Slicer/blob/e1bc774cddc410fe675bcafa390ca44412055f71/Modules/Remote/CMakeLists.txt#L32

For a already configured build tree, the problem will happen as described because the cache option "USE_DWIConvert" is not forced to any value.

To address the issue as it has been reported here, we could force the value of the option. That said, this approach would prevent the user from configuring by setting the option "USE_DWIConvert" directly since its value would always be forced.

Finally, if you consider application like Bender [1] which are based on Slicer, having the option to disable DICOM makes sense.

[2] http://public.kitware.com/Wiki/Bender/Documentation/1.1/Tutorial

pieper

pieper

2014-02-05 13:47

administrator   ~0010564

Yes, makes sense.

Let's make it that BRAINSTools is automatically disabled if DICOM support is turned off.

Jc, would you mind doing this? I'm sure you know exactly how it should be done ;)

jcfr

jcfr

2014-05-14 12:24

administrator   ~0011853

Commit r22907 move the setting of BRAINS option at the superbuild level. It means that switching option Slicer_BUILD_DICOM_SUPPORT ON/OFF will effectively set the option USE_DWIConvert and reconfigure brains appropriately.

See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=22907

Issue History

Date Modified Username Field Change
2013-04-05 07:33 pohl New Issue
2013-04-05 07:33 pohl Status new => assigned
2013-04-05 07:33 pohl Assigned To => hjmjohnson
2013-04-05 07:33 pohl File Added: blub.log
2014-01-06 16:13 hjmjohnson Assigned To hjmjohnson => pieper
2014-01-06 16:15 hjmjohnson Note Added: 0010482
2014-01-07 02:48 pieper Note Added: 0010484
2014-02-04 10:20 pieper Note Added: 0010559
2014-02-04 10:35 jcfr Assigned To pieper => jcfr
2014-02-04 10:35 jcfr Target Version => Slicer 4.4.0
2014-02-05 12:14 jcfr Note Added: 0010561
2014-02-05 12:14 jcfr Status assigned => feedback
2014-02-05 13:47 pieper Note Added: 0010564
2014-05-14 12:24 jcfr Note Added: 0011853
2014-05-14 12:24 jcfr Status feedback => resolved
2014-05-14 12:24 jcfr Fixed in Version => Slicer 4.4.0
2014-05-14 12:24 jcfr Resolution open => fixed
2014-09-17 22:57 jcfr Status resolved => closed