Thanks.
As a development suggestion for 'fslview', it would be useful if there
was an option within 'fslview' to force a proper radiological display
for non-"LAS" or "RAS" oriented files, rather than having to apply
'fslswapdim' to the file itself beforehand. For example, FreeSurfer's
'tkmedit' viewer displays volumes in the expected manner, regardless of
the "orientation" format of the raw data.
cheers,
Mike H.
On Wed, 2009-11-04 at 09:51 -0600, Vy Dinh wrote:
> Hi Matthew,
>
>
> Please refer to FSL's web page for information on how to change the
> orientation. #6 & #7 of this page
> (http://www.fmrib.ox.ac.uk/fslfaq/#general_radiologicaldef) should
> address your concerns. I had this problem myself with the
> coregistrations to standard space of some of my some of my subjects.
> For some unknown reason, some of our subjects were in neurological
> convention, so changing the orientation using fslswapdim and fslorient
> -swaporient rectified our problems.
>
>
> -Vy
>
> On Wed, Nov 4, 2009 at 9:10 AM, Matthew Webster
> <[log in to unmask]> wrote:
> Hi,
> You can use the fslswapdim tool ( and fslorient if
> necessary ) to change the orientation of your image.
> Many Regards
>
> Matthew
>
> Hello,
> I have an nii T1w volume with "PIR" orientation.
> i.e., using 'fslhd', I get:
>
> qform_xorient Anterior-to-Posterior
> qform_yorient Superior-to-Inferior
> qform_zorient Left-to-Right
>
> When I load this volume into 'fslview', the directions
> (R,L,A,P,S,I) are
> labeled correctly, but the display itself is sideways
> or upside down.
> e.g., the coronal view is displayed with the S -> I
> axis running left to
> right on the screen (sideways), and the sagittal view
> has the S -> I
> axis running from bottom to top (upside down).
>
> Is there a way to have 'fslview' display this volume
> in a conventional
> "radiological" display, or is it limited to displaying
> according to the
> ordering of the raw (i,j,k) data?
>
> thanks,
> Mike H.
>
>
> --
> Michael Harms, Ph.D.
> --------------------------------------------------------------------
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> Renard Hospital, Room 6615 Tel: 314-747-6173
> 660 South Euclid Ave. Fax: 314-747-2182
> St. Louis, MO 63110 Email:
> [log in to unmask]
> --------------------------------------------------------------------
>
>
>
>
> --
> Vy T.U. Dinh
> Research Assistant, Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853
> Email: [log in to unmask]
>
>
>
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