When you select the files to re-orient, you will need to select the
volumes within the 4D file to change the orientation of. This
involves changing the filter in the file selector from "1" to eg
"1:1000", to allow you to select blah.nii,1 blah.nii,2 etc
The NIfTI headers only have space for a single (complete) affine
transformation matrix, which is not ideal for motion corrected fMRI
data etc. For SPM, my solution to this was to generate a separate
.mat file containing the orientations of the various 3D volumes within
the NIfTI file. If this .mat file exists, all the orientations of the
various volumes (other than the first) will be read from the .mat. If
it doesn't exist, all the orientations will be the same as that of the
first.
I think in your case, you should be able to delete (or rename) the
.mat file so that all volumes have the same orientation as the first.
All the best,
-John
On 4 January 2012 16:27, S.F.W. Neggers <[log in to unmask]> wrote:
> Dear all,
>
> I need to reorient (no reslice, header change only) a 4D nifti file.
> I tried to reorient my 4D nifti file in SPM8, with display (or the batch
> utils), using a pitch of 90 deg (pi/2 rad). It appeared only the first image
> in this 4D nifti file had a header that was reoriented, the 2nd till last
> had the old orientation.
>
> I verified this by doing
>
> fname='some4Dfile.nii';
> V=spm_vol(fname);
>
>
> then, V(1).mat had changed, but V(2).mat and onwards didnt.
>
> With
>
> Data=spm_read_vols(V);
> for t=2:length(V)
> V(t).mat=V(1).mat;
> end
> spm_write_vols(V,Data);
>
> I couldnt fix this, as apparently spm_write_vols cant write 4D data.
>
> Any ideas?
>
> Cheers,
>
> Bas
>
> --
> --------------------------------------------------
> Dr. S.F.W. Neggers
> Division of Brain Research
> Rudolf Magnus Institute for Neuroscience
> Utrecht University Medical Center
>
> Visiting : Heidelberglaan 100, 3584 CX Utrecht
> Room B.01.1.03
> Mail : Huispost B01.206, P.O. Box 85500
> 3508 GA Utrecht, the Netherlands
> Tel : +31 (0)88 7559609
> Fax : +31 (0)88 7555443
> E-mail : [log in to unmask]
> Web : http://www.neuromri.nl/people/bas-neggers
> : http://www.neuralnavigator.com (CEO)
> --------------------------------------------------
>
>
> ------------------------------------------------------------------------------
>
> De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
> uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
> ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct
> te informeren door het bericht te retourneren. Het Universitair Medisch
> Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de
> W.H.W.
> (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd
> bij
> de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
>
> Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
>
> ------------------------------------------------------------------------------
>
> This message may contain confidential information and is intended
> exclusively
> for the addressee. If you receive this message unintentionally, please do
> not
> use the contents but notify the sender immediately by return e-mail.
> University
> Medical Center Utrecht is a legal person by public law and is registered at
> the Chamber of Commerce for Midden-Nederland under no. 30244197.
>
> Please consider the environment before printing this e-mail.
|