Hi Alle,
I'm working on eliminating some of these problematic dependencies (slow going for a primarily Windows programmer like myself). Meanwhile, you can try running the Windows version under an emulator such as wine.
Jolinda
On Wed, 16 May 2007 09:23:28 +0100, Alle Meije Wink <[log in to unmask]> wrote:
> Hi Jolinda,
>
> Well as it turns out my nice script is not the solution in the end... Coronal slices are turned into axial slices and all orientation information is lost...
>
> Unfortunately, MRIconvert is one of the programs that I tried and just didn't work. When I unzipped the program in a separate directory (and after "chmod +x MRIconvert"), this is what I got:
>
> [amw71@bcni3 mriconvert]$ pwd
> /home/amw71/usr/local/mriconvert
> [amw71@bcni3 mriconvert]$ ls
> dicom.txt excite.txt fileformats.txt mcverter MRIConvert numaris.txt
> [amw71@bcni3 mriconvert]$ MRIConvert
> MRIConvert: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory
>
> I have a Red Hat flavour of linux, but the naming of the libraries is just that little bit different... Is there a statically linked program available, or sources (with the configure, make, make install option)?
>
> If your
program does the orientation trick, that is by far the best option to use!
>
> Cheers
> Alle Meije
>
> Jolinda Smith <[log in to unmask]> wrote: I think Benny Liberg mentioned MRIConvert already, but I'll mention it again. It will take a directory full of files and sort them into the appropriate volumes automatically. It does use the DICOM image orientation information to correctly align the slices. If you find it does not sort your data correctly, let me know and I will be happy to fix it. It includes a command line utility (for Windows or linux) so it is scriptable. You can get it at lcni.uoregon.edu/~jolinda/MRIConvert. I also have a little command-line utility (DicomSorter) that reads a directory of dicom files and sorts it into subject, study, and series. You might find that useful.
>
> Benny says it has some problems with his
mprage images, but we certainly haven't observed this at our site. I'm still waiting for him to provide me with some example data so I can investigate.
>
> Jolinda
>
> --
> Jolinda Smith
> MR Physicist
> Lewis Center for Neuroimaging
> University of Oregon
> Eugene, OR 97403
> [log in to unmask]
>
> On Tue, 15 May 2007 15:25:46 +0100, Alle Meije Wink wrote:
> > Hi Ged,
> >
> > Thanks for that info!
> >
> > > Going from DICOM to NIfTI via Analyze like this loses the orientation
> > > information in the DICOM fields (e.g. ImagePatientPosition, etc)
> > > [snip]
> > > Some of the direct DICOM->NIfTI programs set the NiFTI qform from the
> > > DICOM fields (although, when I checked this, a couple of them were
> > > inconsistent, so do take care!) I think these programs try this:
> > > - dcm2nii
> > > - SPM5 DICOM import
> > > - dinifti
> > > -
possibly LONI Debabaler and others
> > > Links to all these are at the bottom of Chris Rorden's dcm2nii page:
> > > http://www.sph.sc.edu/comd/rorden/mricron/dcm2nii.html
> >
> > I have tried a few of these, but most of them seem to expect volume/4D
> > files to begin with or simply didn't work. In the DICOMDIR setting,
> > scripting it together and having medcon make the volumes, was the best
> > way I could convert whole batches of files from a CD.
> >
> > Plus, are you sure that these programs estimate the position of a volume
> > using the positions of individual slices?
> >
> > I tried the links, but none of them actually gave useful information in
> > terms of: this is your DICOM cd, and this is how you rip your volumes
> > off it...
> >
> > Any advice is still much appreciated, and if those programs really come
> > up with Q-forms from slice data, I'm very impressed!
> >
> > bw
> > Alle Meije
> >
>
>
>
>
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