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