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

From: Vasilis Vlachoudis <Vasilis.Vlachoudis_at_cern.ch>
Date: Thu, 13 Nov 2014 20:19:19 +0000

It might be a problem in the pydicom library used on Ubuntu. On Fedora it works ok.
Could you try to install the latest version of pydicom an alternative way is to use the command
easy_install pydicom
that will install the latest version for your distribution

V.

________________________________________
From: Francesco Collamati [francesco.collamati_at_roma1.infn.it]
Sent: 13 November 2014 15:08
To: Francesca Fiorini
Cc: Vasilis Vlachoudis; fluka-discuss_at_fluka.org
Subject: Re: [fluka-discuss]: Re: error in cropping CT in Flair

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 - 22:38:04 CET