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IDProjectCategoryView StatusDate SubmittedLast Update
0001969Slicer4Module DICOMpublic2012-05-02 09:402014-03-06 05:55
Reporterkirbyju Assigned Topieper  
PrioritynormalSeveritymajorReproducibilityalways
Status closedResolutionfixed 
Product VersionSlicer 4.1.0 
Target VersionSlicer 4.2.0Fixed in VersionSlicer 4.4.0 
Summary0001969: can't import dicom images
Description

After starting Slicer, from "Welcome to Slicer" module:

1) Click "Load DICOM Data"
2) Click "Import"
3) Select folder with DICOM objects in it
4) Click "Import"

I always receive a popup dialogue box stating the following:

The database file path "./ctkDICOM-Database/ctkDICOM.sql" cannot be opened.

If I click OK, then "Show DICOM Browser" to try again I do not get any more popups but the images still do not import and I can see in my terminal the following error repeating for each image that was in the directory:

Processing /home/kirbyju/Pictures/PROSTATE-DIAGNOSIS/ProstateDx-01-0021/1.3.6.1.4.1.14519.5.2.1.4792.2002.119570163000912331050065782444/000001/000025.dcm
QSqlQuery::prepare: database not open
SQLITE ERROR: Parameter count mismatch

Additional Information

$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 11.04
Release: 11.04
Codename: natty

$ uname -a
Linux nci-kirbyju-linux 2.6.38-14-generic 0000058-Ubuntu SMP Tue Mar 27 20:04:55 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

TagsNo tags attached.

Relationships

related to 0002406 closedpieper DICOM module not usable first time Slicer is run on fresh Slicer install 
related to 0001655 closedjcfr Allow different module paths definition for each Slicer instance 

Activities

kirbyju

kirbyju

2012-05-02 11:52

reporter   ~0004125

I just tried running slicer with sudo and it works. Perhaps there is some way to avoid having to do this?
pieper

pieper

2012-05-02 13:13

administrator   ~0004126

Hi -

You can chose the database directory by browsing to a location of your choice with the button labeled "Local Database" in the dicom study browser. If you pick a directory where you have right access this should allow you to avoid using 'sudo'.

Please add a note if that works for you - we can change the behavior of the module to give a dialog if it can't save in the currently selected directory.

-Steve
kirbyju

kirbyju

2012-05-03 05:42

reporter   ~0004145

I see the button you mentioned. The full path is:

/home/kirbyju/Slicer-4.1.0-linux-amd64/ctkDICOM-Database/

As a test I deleted my Slicer installation and started fresh. I ran Slicer without sudo, and the default directory for the local database is the same as above.

When the error occurred I checked and no directory was created in this location. I then created a directory from the dialogue box that pops up called "DICOM-Data" and chose this as the location for the Local Database. This worked correctly so I believe the problem is that Slicer is just having problems with automatically creating the ctkDICOM-Database directory if it doesn't yet exist.
pieper

pieper

2012-07-30 05:04

administrator   ~0005444

Things should be clearer after rev 20713

http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=20713
kirbyju

kirbyju

2012-08-02 09:38

reporter   ~0005490

When I just extracted the new release to a new directory and ran Slicer (nightly) it somehow remembered my settings from the Slicer (stable) release. So I deleted both directories completely and extracted Slicer (nightly) again in an attempt to fully recreate the issue on the new release. Upon clicking "Load DICOM Data" I got the following error:

The database file path "/home/kirbyju/Slicer-4.1.0-linux-amd64/DICOM-Database/ctkDICOM.sql" cannot be opened.

After hitting OK on that error it presents the DICOM Details popup window. I clicked Import and selected a directory containing DICOM images. It looked like it worked but nothing showed up in the DICOM Details window afterwards. No error message either.

So then I clicked the Local Database button, and created a directory called DICOM-Database and set this to be my LocalDatabase folder. Now importing works.

I think it would be ideal if Slicer could just automatically create this directory if it's not found when you first click the Load DICOM Data but it appears something still prevents this from happening naturally.
pieper

pieper

2012-08-22 05:19

administrator   ~0005679

Fixed in r20817

One of the issues reported in the notes (that the wrong dicom directory persists across reinstalls) is related to this issue and needs to be solved on an application-wide basis.

http://na-mic.org/Bug/view.php?id=1655
jcfr

jcfr

2014-03-06 05:07

administrator   ~0010953

Closing resolved issues that have not been updated in more than 3 months

Issue History

Date Modified Username Field Change
2012-05-02 09:40 kirbyju New Issue
2012-05-02 09:40 kirbyju Status new => assigned
2012-05-02 09:40 kirbyju Assigned To => pieper
2012-05-02 11:52 kirbyju Note Added: 0004125
2012-05-02 13:13 pieper Note Added: 0004126
2012-05-02 13:13 pieper Status assigned => feedback
2012-05-03 05:42 kirbyju Note Added: 0004145
2012-05-18 06:33 pieper Target Version => Slicer 4.2.0 AHM Summer 2012
2012-07-30 05:04 pieper Note Added: 0005444
2012-07-30 05:04 pieper Resolution open => fixed
2012-08-02 09:38 kirbyju Note Added: 0005490
2012-08-22 04:57 pieper Relationship added related to 0002406
2012-08-22 05:17 pieper Relationship added related to 0001655
2012-08-22 05:19 pieper Note Added: 0005679
2012-08-22 05:19 pieper Status feedback => resolved
2014-03-06 05:07 jcfr Note Added: 0010953
2014-03-06 05:10 jcfr Status resolved => closed
2014-03-06 05:55 jcfr Fixed in Version => Slicer 4.4.0