Difference between revisions of "Developer Meetings/20140610"
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* Open discussion, Q&A | * Open discussion, Q&A | ||
* Discussion on GUI issue with DWIConverter module for Nrrd to FSL conversion | * Discussion on GUI issue with DWIConverter module for Nrrd to FSL conversion | ||
| + | |||
| + | - we ran the DWIConverter from the command line, and the conversion from Nrrd to Nifti went well. | ||
| + | - it would be great if the GUI was working too . | ||
| + | |||
| + | The two ‘…’ button do not work: both of them pop up a window named 'Open a File' that let doesn't let the user create a new file. | ||
| + | > | ||
| + | > I followed your suggestion and entered a full path for the bvec and bvals files (please see the GUI screenshot). | ||
| + | > | ||
| + | > The good news if that the bvec and bvals files got written in the directory! However, the resulting nifti file is empty and I get the error message: | ||
| + | > | ||
| + | > | ||
| + | > ERROR: In /Users/kitware/Dashboards/Nightly/Slicer4/Libs/vtkTeem/vtkNRRDReader.cxx, line 425 | ||
| + | > | ||
| + | > vtkNRRDReader (0x13fb74690): Error reading /var/folders/7k/pwsk6_bd2tg9g58l7j_2d3cr0000gn/T/Slicer/BDGAC_vtkMRMLDiffusionWeightedVolumeNodeC.nrrd: only 3D/4D volumes supported | ||
| + | > | ||
| + | > | ||
| + | > Any idea why this happens ? | ||
| + | > | ||
| + | > Thanks again for your help, | ||
| + | > | ||
| + | > Sonia | ||
| + | > | ||
| + | > | ||
| + | > On 6/6/14, 1:15 PM, Williams, Norman K wrote: | ||
| + | >> I just discussed this issue with Hans, and I’m not sure what the solution is exactly. But looking at the command line there seems to be an issue with the SlicerExecutionModel handling of the Bval and Bvec filenames. They are defined as ‘files’ with respect to SEM: | ||
| + | >> <parameters> | ||
| + | >> <label>NrrdToFSL Parameters</label> | ||
| + | >> <description><![CDATA[NrrdToFSL Parameters]]></description> | ||
| + | >> <file> | ||
| + | >> <name>outputBValues</name> | ||
| + | >> <longflag>--outputBValues</longflag> | ||
| + | >> <label>B Values File</label> | ||
| + | >> <channel>output</channel> | ||
| + | >> <description><![CDATA[B Values text file]]></description> | ||
| + | >> </file> | ||
| + | >> <file> | ||
| + | >> <name>outputBVectors</name> | ||
| + | >> <longflag>--outputBVectors</longflag> | ||
| + | >> <label>B Vector File</label> | ||
| + | >> <channel>output</channel> | ||
| + | >> <description><![CDATA[B Vector text file]]></description> | ||
| + | >> </file> | ||
| + | >> </parameters> | ||
| + | >> | ||
| + | >> Hans pointed out that if you simply enter the filename for the Image output, when the command line is built for DWIConvert, it includes a full path, but when you do the same thing for these two parameters, it just includes whatever filename is in the dialog. This doesn’t make sense; it’s as though it treats file SEM variables the same as string variables. | ||
| + | >> | ||
| + | >> If you don’t have a full path as part of the filename, then your file will be written to whatever directory is current in Slicer & the inferior DWIConver process. | ||
| + | >> | ||
| + | >> It seems like a bug also that there are two ‘…’ buttons in the GUI panel, I haven’t looked at how SEM works to build panels. | ||
| + | >> | ||
| + | >> Sonia — you should try clicking on the ‘…’ button — I’d go with the one closest to the file name in the user interface — and navigate to the directory in which you want the files created. Then you type a filename into the dialog. If things are working correctly, then the full path to the output files will show up in the Slicer DWIConvert dialog. Otherwise this is a bug in Slicer SEM processing. | ||
Revision as of 18:19, 10 June 2014
Home < Developer Meetings < 20140610To discuss
- Review Roadmap and issue tracker
- Open discussion, Q&A
- Discussion on GUI issue with DWIConverter module for Nrrd to FSL conversion
- we ran the DWIConverter from the command line, and the conversion from Nrrd to Nifti went well. - it would be great if the GUI was working too .
The two ‘…’ button do not work: both of them pop up a window named 'Open a File' that let doesn't let the user create a new file.
> > I followed your suggestion and entered a full path for the bvec and bvals files (please see the GUI screenshot). > > The good news if that the bvec and bvals files got written in the directory! However, the resulting nifti file is empty and I get the error message: > > > ERROR: In /Users/kitware/Dashboards/Nightly/Slicer4/Libs/vtkTeem/vtkNRRDReader.cxx, line 425 > > vtkNRRDReader (0x13fb74690): Error reading /var/folders/7k/pwsk6_bd2tg9g58l7j_2d3cr0000gn/T/Slicer/BDGAC_vtkMRMLDiffusionWeightedVolumeNodeC.nrrd: only 3D/4D volumes supported > > > Any idea why this happens ? > > Thanks again for your help, > > Sonia > > > On 6/6/14, 1:15 PM, Williams, Norman K wrote: >> I just discussed this issue with Hans, and I’m not sure what the solution is exactly. But looking at the command line there seems to be an issue with the SlicerExecutionModel handling of the Bval and Bvec filenames. They are defined as ‘files’ with respect to SEM: >> <parameters> >> <label>NrrdToFSL Parameters</label> >> <description><![CDATA[NrrdToFSL Parameters]]></description> >> <file> >> <name>outputBValues</name> >> <longflag>--outputBValues</longflag> >> <label>B Values File</label> >> <channel>output</channel> >> <description><![CDATA[B Values text file]]></description> >> </file> >> <file> >> <name>outputBVectors</name> >> <longflag>--outputBVectors</longflag> >> <label>B Vector File</label> >> <channel>output</channel> >> <description><![CDATA[B Vector text file]]></description> >> </file> >> </parameters> >> >> Hans pointed out that if you simply enter the filename for the Image output, when the command line is built for DWIConvert, it includes a full path, but when you do the same thing for these two parameters, it just includes whatever filename is in the dialog. This doesn’t make sense; it’s as though it treats file SEM variables the same as string variables. >> >> If you don’t have a full path as part of the filename, then your file will be written to whatever directory is current in Slicer & the inferior DWIConver process. >> >> It seems like a bug also that there are two ‘…’ buttons in the GUI panel, I haven’t looked at how SEM works to build panels. >> >> Sonia — you should try clicking on the ‘…’ button — I’d go with the one closest to the file name in the user interface — and navigate to the directory in which you want the files created. Then you type a filename into the dialog. If things are working correctly, then the full path to the output files will show up in the Slicer DWIConvert dialog. Otherwise this is a bug in Slicer SEM processing.
