Hi Kumar,

It doesn't sound like you've got a problem with the conversion.
I suspect that you are just unhappy with the way around that
FSLView is showing the data. This is perfectly fine, as FSLView
chooses to show the data as the scanner acquired it, so that
sagittal, coronal and axial scans look quite different. Each part
of the FSLView window could show any of the views, in any
orientation - that is not a problem. As long as the *labels*
are correctly attached to the views then the nifti file is correct
and you do not need to do any of the things that Todd suggests.

If you want to reorient your image so that FSLView shows it
in the same way that the standard template images are shown
then you can do the following:
   fslorient MYIMAGE
and if the result is "RADIOLOGICAL" then do:
   fslswapdim MYIMAGE RL PA IS MYIMAGE
else do:
   fslswapdim MYIMAGE LR PA IS MYIMAGE

This will perform a 90, 180 or 270 degree rotation
on the image to make it display the same way
around as the MNI152 images in FSLView.

I hope this helps.
All the best,
Mark




On 28 Jun 2010, at 21:48, Todd L. Richards wrote:

> Kumar,
> With our Philips Scanner, I usually use the PAR/REC output files not
> the nii output from Philips.
> Another option is using the dicom files and then converting them
> using dcm2nii which is part the software package
> from MRICRON.
> What output files are you using?
> Todd
>
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Adityakumar Kasinadhuni
> Sent: Monday, June 28, 2010 12:52 PM
> To: [log in to unmask]
> Subject: [FSL] Re : Image distortion
>
>
> Hi,
>
> This is Kumar. I tried to open images that I had obtained from a
> Philips Scanner (.nii format) using fslview. However the images did
> not show up in the proper convention, or at least that's what I
> think. Can anyone please help me out in this matter? Is there
> anything else that needs to be done before opening our data first
> time in fslview.
> I have just migrated from using BVQX to FSL and in BV, it used to
> pop up an option if I would like to have it in the BV convention. Is
> there any such thing that needs to be done with FSL as well?
>
> P.S : I am not sure if the above was very helpful, but just to clear
> things, the sagittal image seems to be in the right orientation,
> however the anterior and posterior of the axial plane point from
> side to side (as opposed to the usual top and down in 2d view). The
> same goes with the coronal view as well. So I was wondering if there
> is something that could be done to fix this?
>
> Thank you.
>
> --
> Aditya Kumar. K
> Grad Student,
> Department of BME
> UF.