The problem is not with SPM.  The xform_nii.m function you are using
(which I found on the web) doesn't seem to be able to handle the whole
range of NIfTI functionality.  In particular, it expects there to be
no rotations (other than some combination of 90 degree rotations or
flips) in the image headers.  The email address of the author is in
the xform_nii.m file, so you could perhaps ask him for advice.

Best regards,
-John


On 3 June 2013 13:49, Karin Lundengård <[log in to unmask]> wrote:
> Hi!
>
> Thank you Iwo for your advise.
>
> However, I think swaping to a new program at this stage would be a bit of a problem in our group, so if there is any solution where I can still use my SPM-iages that would be for the best.
>
> Is there anyone else with experience in this?
>
>
> Karin Lundengård IMH
>
>
> Best regards
>
> Karin Lundengård
>
> PhD-student
>
>
> CMIV
>
> Department of Medical and Health Sciences
>
> Linköping University
>
> SE-581 85 Linköping
>
> SWEDEN
>
>
> Phone: (+46) 013-281010
>
> Visiting address: CMIV, Entrance 7, Elevator A, 11th floor, Campus US
>
> www.imh.liu.se
>
> www.imh.liu.se/radiologiska-vetenskaper
>
>
> ________________________________________
> Från: Iwo Bohr [[log in to unmask]]
> Skickat: den 3 juni 2013 13:57
> Till: Karin Lundengård; [log in to unmask]
> Ämne: RE: [SPM] reslice
>
> Hi,
>
> Hello,
>
> I had the same problem with images preprocessed in SPM8.
>  However when I set up a new workflow (starting with the Philips parec native format; I don't know if it is necessary to go that far ) and then doing the preprocessing in FSL, the problem disappeared.
> I don't know if there is any work-around this problem for SPM-preprocessed images maybe somebody knows?
>
> Best wishes,
>
> Iwo
>
>>-----Original Message-----
>>From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
>>On Behalf Of Karin
>>Sent: 03 June 2013 12:46
>>To: [log in to unmask]
>>Subject: [SPM] reslice
>>
>>Hi!
>>
>>I would like to open my images which I have realiged and resliced in spm as
>>matrices in matlab.
>>
>>To do this I am using load_nii. However, this only works on half of them. The
>>others give me the following error message:
>>
>>
>>??? Error using ==> xform_nii>change_hdr at 350
>>
>>
>>   Non-orthogonal rotation or shearing found inside the affine matrix
>>   in this NIfTI file. You have 3 options:
>>
>>   1. Using included 'reslice_nii.m' program to reslice the NIfTI
>>      file. I strongly recommand this, because it will not cause
>>      negative effect, as long as you remember not to do slice
>>      time correction after using 'reslice_nii.m'.
>>
>>   2. Using included 'load_untouch_nii.m' program to load image
>>      without applying any affine geometric transformation or
>>      voxel intensity scaling. This is only for people who want
>>      to do some image processing regardless of image orientation
>>      and to save data back with the same NIfTI header.
>>
>>   3. Increasing the tolerance to allow more distortion in loaded
>>      image, but I don't suggest this.
>>
>>   To get help, please type:
>>
>>   help reslice_nii.m
>>   help load_untouch_nii.m
>>   help load_nii.m
>>
>>Error in ==> xform_nii at 154
>>   [hdr,orient]=change_hdr(hdr,tolerance,preferredForm);
>>
>>Error in ==> load_nii at 135
>>   nii = xform_nii(nii, tolerance, preferredForm);
>>
>>
>>
>>None of the images gives me any error messages in spm. Can I still trust the
>>results of the spm correlation analysis then?
>>
>>Regarding the problem of opening them as matrices: Can this be solved? I
>>have tried reslice_nii, but that changes the dimensions of the image, which I
>>do not want it to do (the images resliced in spm have the same dimensions as
>>the orginal image).
>>
>>Is there any other command of function I can use in order to open the
>>images?
>>
>>Grateful for any help,
>>Karin