Re: [fluka-discuss]: Re: error in cropping CT in Flair

From: Francesco Collamati <francesco.collamati_at_roma1.infn.it>
Date: Thu, 13 Nov 2014 15:08:55 +0100

Ciao Francesca
regrettably, I do not have a solution for your problem, but on the contrary it is a problem that I have been facing for a while, on my Ubuntu 13 virtual machine on Parallels.
At the end, after trying several things with the python library, I surrendered and I installed a second virtual machine with Fedora, where the (much useful) crop function works like a charm.
So now I use this OS just to crop my dicom and create the .vxl file, than I copy it to ubuntu for all the rest of the processes..
Just to tell that you’re not the only one experiencing this problem!
Francesco
> Il giorno 12/nov/2014, alle ore 15:54, Francesca Fiorini <francesca.fiorini_at_oncology.ox.ac.uk> ha scritto:
>
> Hi Vasilis,
>
> This error appears with every Flair project I open, even with empty ones, and so in these cases the .flair is empty, because I am only using it to produce the vxl file.
>
> Thanks
> Francesca
>
> Francesca Fiorini, PhD
> CRUK and MRC Oxford Institute for Radiation Oncology
> Old Road Campus Research Building
> Off Roosevelt Drive
> University of Oxford
> Oxford, OX3 7DQ
> UK
>
>
>
>
> On 12 Nov 2014, at 12:53, Vasilis Vlachoudis <Vasilis.Vlachoudis_at_cern.ch> wrote:
>
> Hi Francesca,
>
> it seems that something is wrong on the column/row number of the cropping.
> Could you send us the .flair file
> V.
>
>
> ________________________________________
> From: owner-fluka-discuss_at_mi.infn.it [owner-fluka-discuss_at_mi.infn.it] on behalf of Francesca Fiorini [francesca.fiorini_at_oncology.ox.ac.uk]
> Sent: 12 November 2014 10:48
> To: fluka-discuss_at_fluka.org
> Subject: [fluka-discuss]: error in cropping CT in Flair
>
> Dear Vasilis and Fluka/Flair experts,
>
> I am having problems trying to crop CT in Flair. I have done it other times, but now, after either the OS update or Flair update, it does not seem to work any more.
> When I crop the CT and then go to the Voxel page, the "Analyzing slices" window doesn't start. Then when I close Flair, the Flair Error Reporting window appears and says:
>
> Version : 2.0-5
> geoviewer : 2.0-5 False
> Revision : 3314
> Last Change : 2014-10-20 14:11:03
> dicom : 0.9.8
> numpy : 1.8.2
> Platform : linux2
> Python : 2.7.5 (default, Nov 3 2014, 14:26:24)
> [GCC 4.8.3 20140911 (Red Hat 4.8.3-7)]
> TkVersion : 8.5
> TclVersion : 8.5
>
> Traceback:
> Traceback (most recent call last):
> File "/usr/local/flair/tkFlair.py", line 1249, in __call__
> return self.func(*args)
> File "/usr/local/flair/FlairRibbon.py", line 294, in changeTab
> self.activeTab.activate()
> File "/usr/local/flair/VoxelTab.py", line 340, in activate
> if self.page.loadDicom():
> File "/usr/local/flair/DicomPage.py", line 253, in loadDicom
> err = self._loadDicom()
> File "/usr/local/flair/DicomPage.py", line 285, in _loadDicom
> if not self.dicom._scanSlice(os.path.join(path,fn)):
> File "/usr/local/flair/Dicom.py", line 717, in _scanSlice
> self.__scanSliceData(dataset.pixel_array)
> File "/usr/local/flair/Dicom.py", line 742, in __scanSliceData
> array = data[self.rowFrom:self.rowTo+1, self.colFrom:self.colTo+1]
> IndexError: invalid slice
>
> Do you know what the problem might be? Do I have something wrong with the python libraries?
> The other times I used the cropping function, it was with the same CT, so I don't think there is something wrong with it.
>
> Thanks in advance
> Francesca
>
>
> Francesca Fiorini, PhD
> CRUK and MRC Oxford Institute for Radiation Oncology
> Old Road Campus Research Building
> Off Roosevelt Drive
> University of Oxford
> Oxford, OX3 7DQ
> UK
>
> <ct_crop_test.flair><ct_crop_test.inp>
Received on Thu Nov 13 2014 - 16:53:32 CET

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