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
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