Hello,

There is of course the last resort of deleting the orientation and re-assigning it. This (as mentioned on FSL's pages) is generally a last resort, as getting the L-R orientation can be very difficult. If your subjects have a marker to indicate LR, this can be a rather simple method.

See fslswapdim and fslorient, if interested.

http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fslutils

On Sun, Nov 2, 2014 at 4:17 AM, elahe' yargholi <[log in to unmask]> wrote:

Thanks.
I read its manual, it only speaks about converting dcm to nii, but my main problem is converting 1142 3D nii images to 4D nii. Any suggestion?


I do appreciate your attention.

BR,
Elahe'

On Sun, Nov 2, 2014 at 10:01 AM, Stephen Smith <[log in to unmask]> wrote:
Hi - try Chris Rorden's latest and greatest conversion tool:
Cheers


On 2 Nov 2014, at 05:07, elahe' yargholi <[log in to unmask]> wrote:

Dear FSL experts,

I usually use mricron to convert dicom images to 4D nii, but this time my 4D data has 1142 volumes and mricron did not work so used mri_convert or unpacksdcm from freesurfer. They produced the 4D data, but the anterior-posterior is (left to right) in opposite direction of previous 4D data or MNI atlas and the fsl registration is incorrect. what is the safest way to correct that?



I do appreciate your attention.

BR,
Elahe


---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
[log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------

Stop the cultural destruction of Tibet