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hi, i have also experienced this behavior in a context other than visualization. if a mask file is created or edited then saved it appears flipped when loaded into other applications (MATLAB as well as custom software that disregards orientations entirely). the data array itself seems to be modified on save. thanks, oliver On Thu, Jun 11, 2009 at 8:31 AM, Laura Mancini<[log in to unmask]> wrote: > Hi, > > Regarding this bug, which I have seen on my data as well, just now (I > have fsl 4.0.4 on FedoraCore3) to me it seems a problem in writing the > image rather than in visualising it. In fact I created a mask in the R > hemisphere, saved it, opened the file again and it appeared on the L > hemisphere. Hoping it was only a visualisation problem I ran the > probtrack anyway from this region and the tracts found are correct for > the L hemisphere, not for the right as I think it should be if it was > just a visualisation problem (in my case it's easy to differentiate L > and R since the patient has got a tumour on the R hemisphere which > displaces the tract). > > All the best, > Laura > > > -----Original Message----- > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On > Behalf Of Mark Jenkinson > Sent: 19 May 2009 23:15 > To: [log in to unmask] > Subject: Re: [FSL] FSLView Bug with Neurologically Oriented Images > > > Hi, > > I believe that this is only an issue for FSLView. We have tried to make > all programs in FSL work with either Radiological or Neurological > storage (or a mixture of both) in a seemless way. So there should be no > issue with the rest of FSL. > > All the best, > Mark > > > On 19 May 2009, at 18:19, Satrajit Ghosh wrote: > >> Is this bug an fslview issue or does it percolate through other >> programs? Do the other FSL programs pick up the orientation >> information appropriately from a Nifti qform matrix? Or should we >> always enforce radiological convention on the nifti images. >> >> Cheers, >> >> Satra >> >> >> On Sat, May 16, 2009 at 12:25 AM, Matt Glasser <[log in to unmask]> >> wrote: >> This bug (Display only) occurs with the latest released version of >> FSL, >> FSLView, and for me on Ubuntu Jaunty 64bit. >> >> Thanks, >> >> Matt. >> >> -----Original Message----- >> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On >> Behalf >> Of Dave Flitney >> Sent: Friday, May 15, 2009 3:15 PM >> To: [log in to unmask] >> Subject: Re: [FSL] FSLView Bug with Neurologically Oriented Images >> >> Thanks, Jonas. I'm sorry this is causing trouble for you. Until I >> can repair >> this I recommend that you start analysis by reorienting your initial >> data >> images to ensure that they're stored in radiological order. If your >> data is >> all radiological from the start then you shouldn't have any problems >> - at >> least not due to this mask saving/display flipping bug. >> >> PS it would help immensely if you, and anyone else reporting bugs, >> could >> please include version info for FSL, FSLView and OS. >> ------Original Message------ >> From: Jonas Kaplan >> Sender: FSL - FMRIB's Software Library >> To: [log in to unmask] >> ReplyTo: FSL - FMRIB's Software Library >> Subject: Re: [FSL] FSLView Bug with Neurologically Oriented Images >> Sent: 15 May 2009 20:20 >> >> We are having this same problem. Sometimes when closing and reopening > >> the mask the orientation is correct, but other times it actually saves > >> in the wrong orientation, and the image is still flipped when we >> reopen it. This saved-flipping seems sporadic, while display- >> flipping happens every time. We can of course flip them back, but >> this bug means that we have to double-check every mask we save for >> orientation. >> >> Jonas >> >> ---- >> Jonas Kaplan, Ph.D. >> Research Assistant Professor >> Brain & Creativity Institute >> University of Southern California >> >> >> >> On May 3, 2009, at 11:48 AM, Matt Glasser wrote: >> >> > Michael, >> > >> > In this case the image is saved correctly (both correctly in space >> > and with the correct header), it just that the display in that >> > session of FSLView >> > that is changed. If you remove the mask and reload it from the >> > saved file >> > it looks correct. >> > >> > Peace, >> > >> > Matt. >> > >> > -----Original Message----- >> > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On >> > Behalf Of Michael Hanke >> > Sent: Sunday, May 03, 2009 1:40 PM >> > To: [log in to unmask] >> > Subject: Re: [FSL] FSLView Bug with Neurologically Oriented Images >> > >> > On Sun, May 03, 2009 at 01:25:23PM -0500, Matt Glasser wrote: >> >> When creating a mask and drawing an ROI with a neurologically >> >> oriented image, FSLView will flip the image to the other hemisphere > >> >> after saving >> > and >> >> doing something like creating another mask or locking the file >> >> against editing. The saved file will actually be correctly >> >> oriented, only the >> >> display of it in the current session of FSLView is flipped. >> > >> > And it already does that for a while: >> > >> > http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=450572 >> > >> > >> > Michael >> > >> > -- >> > GPG key: 1024D/3144BE0F Michael Hanke >> > http://apsy.gse.uni-magdeburg.de/hanke >> > ICQ: 48230050 >> >> >> >> Sent using BlackBerryR from Orange >> > > ------------------------------------------------------------------------ > This email is confidential and is intended solely for the person or > Entity to whom it is addressed. If this is not you, please forward the > Message to [log in to unmask] We have scanned this email > before sending it, but cannot guarantee that malicious software is > absent and we shall carry no liability in this regard. > > We advise that information intended to be kept confidential should not > Be sent by email. 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