Dear Martin,
this has to do with the .mat file which is not recognised by MRIcro and other
non-SPM software.
If you want to stick to SPM also when creating your ROIs, have a look at the
spm_orthviews plugins on the SPM extensions page and pick up the latest
version. There is a ROI tool too, which might help you drawing your ROIs. Its
not as fast as MRIcro but it can create ROIs from the "CheckReg" view
of one or
more images.
Hope this helps,
Volkmar
Quoting Martin Zalesak <[log in to unmask]>:
> Dear all,
>
> I am trying to use MRIcro to outline anatomical ROIs. I am using a 3D
> MP-RAGE analyze file that I obtained by using the DICOM toolbox from
> Siemens DICOM files.
>
> When I load the image in SPM2 using Display, it looks fine and I see
> on the three panels:
> a coronal image a sagittal image
> an axial image
>
> When I load the same image in MRIcro, it is all flipped, so I see
> with the three projections:
> an axial image a coronal image turned 90 degrees
> a sagittal image
>
> So MRIcro thinks that sagittal is axial, coronal (turned by 90
> degrees) is sagittal and axial is coronal.
>
> The problem is that I want to outline my ROI on the coronal image but
> I can't do it if the 1, the coronal image is not coronal and 2, the
> coronal image is turned by 90 degrees.
>
> I am wondering if this has something to do with the image.mat file,
> which is as follows:
> 0.0070 0.0062 1.3299 -98.8101
> 0.9421 0.3353 -0.0116 -139.7506
> -0.3354 0.9421 -0.0046 -61.3100
> 0 0 0 1.0000
>
> I tried to use avwswapdim in FSL to swap the dimensions so that it
> looks right in MRIcro but, by doing that, I lose the orientation
> information and the I cannot get the structural image to the same
> orientation where I started from.
>
> I would really appreciate any suggestions or help!
>
> Thank you,
> Martin
>
>
>
> Martin Zalesak, M.Sc.
> PhD Candidate in Medical Engineering
> Harvard-MIT Division of Health Sciences and Technology
> Admissions Building, Rm. # 347
> McLean Hospital
> 115 Mill St.
> Belmont, MA 02478
>
> Phone: (617) 855-2229
> Fax: (617) 855-2895
>
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