Dear Volkmar and others
I have downloaded spm_orthviews for SPM2 and put it
under the file of toolbox. I could not run it under
spm. What am I missing?
Ali
Ege University School of Med
Dept of Psytchiatry
Izmir Turkey
--- Volkmar Glauche
<[log in to unmask]> wrote:
> 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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