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
>
|