Mark,
Thanks for looking at this, the info (or at least, what I think you're
asking for) is below.
Thanks again,
Pat
For the original:
qform_name Scanner Anat
qform_code 1
qto_xyz:1 -3.000000 0.000000 -0.000000 96.000000
qto_xyz:2 0.000000 3.000000 -0.000000 -108.922874
qto_xyz:3 0.000000 0.000000 3.000000 -37.914421
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Unknown
sform_code 0
sto_xyz:1 0.000000 0.000000 0.000000 0.000000
sto_xyz:2 0.000000 0.000000 0.000000 0.000000
sto_xyz:3 0.000000 0.000000 0.000000 0.000000
sto_xyz:4 0.000000 0.000000 0.000000 0.000000
sform_xorient Unknown
sform_yorient Unknown
sform_zorient Unknown
For the swapped:
qform_name Scanner Anat
qform_code 1
qto_xyz:1 3.000000 0.000000 0.000000 -93.000000
qto_xyz:2 0.000000 3.000000 0.000000 -108.922874
qto_xyz:3 0.000000 0.000000 3.000000 -37.914421
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Left-to-Right
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 3.000000 0.000000 0.000000 -93.000000
sto_xyz:2 0.000000 3.000000 0.000000 -108.922874
sto_xyz:3 0.000000 0.000000 3.000000 -37.914421
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Left-to-Right
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
On 1/10/07, Mark Jenkinson <[log in to unmask]> wrote:
> Hi,
>
> Your are right that only fsl3.3 will deal with qforms happily.
> I would remove your old fsl3.2 version so that you don't get confusing
> calls to old versions when paths are setup wrongly.
>
> As for origin change, it does seem weird. Can you send us the
> full qform and sform output (from avwhd) on the pre- and post-images?
>
> All the best,
> Mark
>
>
> On 9 Jan 2007, at 22:05, Pat Vee wrote:
>
> > Hi Tim,
> >
> > Thanks for the quick reply. Sorry, I should have been more clear -
> > I saw the series of emails you're referring to and was trying to
> > follow it, but didn't get the same results. Since sending my 1st
> > email, I figured out that though I thought I was running fsl3.3,
> > the command line script was calling 3.2... So, I've been able to
> > change the orientation by just using avworient -swaporient.
> > However, I wanted to check something, if you don't mind...
> >
> > It's my understanding that reading qform wasn't fully implemented
> > in fsl3.2 and that I was having problems with avworient, since my
> > data had sform info, but "unknown" for qform. Now in fsl3.3, both
> > qform and sform are supported, so avworient can swap
> > appropriately. So, the images look right and are reported in the
> > correct orientation. In swapping the data, the "unknown" in the
> > original data's qform is then replaced with the sform (swapped, of
> > course). However, the numbers that are stored for x, y, z, are
> > slightly different pre- and post-swap. Some signs are revered, as
> > expected - but in the field called "qto_xyz:1" I originally have
> > "-3 0 -0 96" which is changed to "3 0 0 -93" in the swapped image.
> > The values in all the other fields are unchanged. Is this ok?
> >
> > Thanks,
> > Pat
> >
> > On 1/9/07, Tim Behrens < [log in to unmask] > wrote:Hi -
> > This email train a few days ago addresses exactly this problem.
> >
> > http://www.jiscmail.ac.uk/cgi-bin/webadmin?
> > A2=ind0612&L=FSL&P=R16636&I=-3&X=1C7CFF1E9EF73B331C&Y=behrens%
> > 40fmrib.ox.ac.uk
> >
> > If you go through this train to the end, you should be ok.
> >
> > Note that my first reply had a typo error in one of the commands,
> > which Kirk found - so you will need to look through my second reply
> > as well.
> >
> > Cheers
> > T
> >
> >
> > On 9 Jan 2007, at 15:46, Pat Vee wrote:
> >
> > > Hi all,
> > >
> > > I'm using MRIConvert to convert dicom files to nifti format - after
> > > doing
> > > so, I check the orientation with avworient and the images are stored
> > > neurologically. When I try to swap the orientation (avworient -
> > > swaporient
> > > IMAGE) then check again, it says that they're still stored
> > > neurologically.
> > > When I view the images in fslview, the "swapped" is exactly the
> > > same as the
> > > original. If I look at the header, the only difference that I see
> > > is that
> > > the description is changed (from the original description of my
> > > series) to
> > > FSL3.2beta - this itself is confusing, since I have FSL3.3
> > > installed... Any
> > > thoughts on what I might be doing wrong?
> > >
> > > Thanks in advance,
> > > Pat
> >
>
|