On Thu, Mar 25, 2010 at 06:15:36PM -0700, Connolly, Colm wrote:
> On Mar 25, 2010, at 2:46 PM, Michael Hanke wrote:
>
> > Hi,
> >
> > On Thu, Mar 25, 2010 at 08:19:53PM +0000, Greg H wrote:
> >> Dear FSL experts,
> >>
> >> I am a new user of FSL and this is the first time I've collected
> >> data on a Philips 3T scanner. I am using dcm2nii for this
> >> conversion because based on the program it appears that it will
> >> convert these files to nifti format. I noticed that it has some
> >> trouble setting the scaling so some of our files can not be viewed
> >> in fslview. I was able to find the min and max intensities using
> >> fslstats -t image.par -r and then the file can be viewed in
> >> fslview. I am wondering if anyone has had any trouble converting
> >> par files with dcm2nii. Sometimes it looks like it cannot
> >> completely read the par file and I noticed that the cal_min and
> >> cal_max are always set to 0. Does anyone have any suggests as to
> >> why this may happen or what I can do to fix it? Is there a better
> >> program available? I went through the archives, but I didn't find
> >> anything relevant to this problem.
> >
> > I recently started toying with a (from scratch) parrec2nii converter
> > based on nibabel, because people in the department complained about
> > insufficiencies of available software. There is some code already,
> > but right now, I don't expect it to be any less buggy than other
> > tools, but my intentions are good ;-)
> >
> > Maybe it can help you in the future. Or you can help me by testing
> > things out and offer feedback!?
> >
> > The current code is here:
> >
> > http://github.com/hanke/nibabel/blob/mh/master/bin/parrec2nii
> >
> >
> > Michael
> >
> >
> > PS: Right now it will set the scaling to match the method documented
> > in the PAR header. However, Phillips own tools seem to ignore that
> > (there are actually two different scaling values in the header). I
> > will add support to choose between the two possibilities.
>
>
> There is a program called 3dPAR2AFNI.pl which is part of afni which
> will do this job for you. It, however, has some limitations, such as
> only handling axial slices. But you make be able to make there
> relatively minor modifications to it handle other orientations.
It should be mentioned that this is a perl script that serves as a
frontend for other AFNI tools -- so you actually need AFNI too. It also
doesn't handle the more recent "clincial tryout" variant of the 4.2 PAR
images.
Michael
--
GPG key: 1024D/3144BE0F Michael Hanke
http://mih.voxindeserto.de
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