 |
 |
Dear Mark, I was wondering whether this behavior of fslview will be fixed in the near future thanks in advance William On Jun 11, 2009, at 3:57 PM, oliver hinds wrote: > 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. We also advise that health concerns should be >> Discussed with a medical professional in person or by telephone. >> NHS Direct can also provide advice. We shall not be liable for any >> failure to follow this advice. University College London Hospitals >> NHS >> Foundation Trust (UCLH). >>