Hi Darren,
no - the images are not the same and the upper half of the more rostral
slices being chopped off does not seem to be related to the *.mat-file.
Pitching by
-pi/2 does not change the issue. The dimensions are correct, however. But if
you look at the images in MRIcro there is a clear difference to me. At least
from what I can tell, the dicom convertor does NOT work properly (these were
coronally acquired slices).
Andreas
----- Original Message -----
From: "Darren R. Gitelman" <[log in to unmask]>
To: "Andreas Bartsch" <[log in to unmask]>
Cc: <[log in to unmask]>
Sent: Thursday, November 21, 2002 11:49 PM
Subject: Re: AW: Web page
Hi Andreas:
Actually both images are the same but they are rotated with respect to one
another. Take a look at the image dimensions- they are both 64 x 64 x 11.
However, the SPM generated image has been rotated so that it is displayed
correctly. The MRIcro image shows the coronal image in the lower left, the
axial in the upper left and the sagittal on the right. The SPM image has
the axial in the lower left, the coronal in the upper left and the sagittal
on the right. Type -pi/2 in the pitch box and you will see that the spm and
the MRIcro images look the same. Alternatively throw away the *.mat file
on the spm image and it looks the same as the MRIcro image. Unless I'm
mistaken the dicom convertor appears to be working appropriately.
Darren
At 11:11 PM 11/21/2002 +0100, Andreas Bartsch wrote:
>Hi John,
>many congrats for the early release. I guess lots of us have expected it to
>be released a bit later and everyone will appreciate your and the FILs
>efforts.
>And here come the 2nd & 3rd (?) questions on spm2b:
>- I have tried to use the DICOM conversion utility added to spm2b on a
>mosaic file (i.e., the way it gets on the syngo environment - without
having
>exported it to "offline"). The conversion runs through smoothly but the
>upper half part of the image seems to get chopped off except for 1 slice.
>MRIcro does the conversion fine (although you have to change the
z-dimension
>in the header). I am adding the original image file, MRIcro's conversion
and
>SPM2b's in the attached *.zip. What is going on here?
>-Where has the useful HDR edit gone to?
>Best regards-
>Andreas
>***************************************************************************
*
>******************************
>Dr. Andreas J. Bartsch phone: +49 (0)931-201-0
>Division of Neuroradiology,
>ecr.: -34791
>BJMU Wuerzburg pager:
>#5325
>Josef-Schneider-Str. 11 fax: +49 (0)
>931-201-34685
>97080 Wuerzburg email:
>[log in to unmask]
>Germany
>[log in to unmask]
>***************************************************************************
*
>******************************
>
>----- Original Message -----
>From: "John Ashburner" <[log in to unmask]>
>To: <[log in to unmask]>
>Sent: Thursday, November 21, 2002 6:52 PM
>Subject: Re: AW: Web page
>
>
> > > Displaying the same (non-normalized) image from a patient:
> > >
> > > spm99 tumor is on the left
> > > spm2b tumor is on the right
> > >
> > > Have you change the orientation defaults?
> >
> > Check out the compatibility section of the page:
> > http://www.fil.ion.ucl.ac.uk/spm/spm2b.html#Compat
> >
> > Although SPM2b still uses the Analyze file format, and will therefore
> > read image files from previous versions of SPM, there are differences
> > in the algorithms, templates and models used in SPM2 over previous
> > releases. Therefore, we recommend you use a single SPM version for
> > any given project.
> >
> > One thing to watch out for is the image orientation. The proper
> > Analyze format uses a left-handed co-ordinate system, whereas
> > Talairach uses a right-handed one. In SPM99, images were flipped at
> > the spatial normalisation stage (from one co-ordinate system to the
> > other). In SPM2b, a different approach is used, so that either a left-
or
> > right-handed co-ordinate system is used throughout. The SPM2b
> > program is told about the handedness that the images are stored with
> > by the spm_flip_analyze_images.m function and the defaults.analyze.flip
> > parameter that is specified in the spm_defaults.m file. These files are
> > intended to be customised for each site. If you previously used SPM99
> > and your images were flipped during spatial normalisation, then set
> > defaults.analyze.flip=1. If no flipping took place, then set
> > defaults.analyze.flip=0.
> >
> > Check that when using the Display facility (possibly after specifying
> > some rigid-body rotations) that:
> >
> > The top-left image is coronal with the top (superior) of the head
> > displayed at the top and the left shown on the left. This is as if
>the
> > subject is viewed from behind.
> >
> > The bottom-left image is axial with the front (anterior) of the
> > head at the top and the left shown on the left. This is as if the
> > subject is viewed from above.
> >
> > The top-right image is sagittal with the front (anterior) of the
> > head at the left and the top of the head shown at the top. This is
>as
> > if the subject is viewed from the left.
> >
> > Best regards,
> > -John
> >
> > --
> > Dr John Ashburner.
> > Functional Imaging Lab., 12 Queen Square, London WC1N 3BG, UK.
> > tel: +44 (0)20 78337491 or +44 (0)20 78373611 x4381
> > fax: +44 (0)20 78131420 http://www.fil.ion.ucl.ac.uk/~john
> >
-------------------------------------------------------------------------
Darren R. Gitelman, M.D.
Cognitive Neurology and Alzheimer¹s Disease Center
E-mail: [log in to unmask]
WWW: http://www.brain.northwestern.edu
Voice: (312) 908-9023
Fax: (312) 908-8789
Northwestern Univ., 320 E. Superior St., Searle 11-470, Chicago, IL 60611
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