Hi Ged,
> I've used SPM5's DICOM import and dinifti with a bunch of unsorted DICOM
> slices (not a DICOMDIR, but I think it should be similar) rather than
I guess so, because now I had to gather and sort the slices myself as
well. By the looks of it though dinifti looks less automated than medcon.
The reasons that I have saved SPM5 until last are: the fact that it's
not scriptable (well, matlab.. sort of..) and the fear of ruining
everything with .mat files!
> volumes, and they seemed to work fine (though as I mentioned some DICOM
> data ended up with different NIfTI qforms depending on the program --
> something I keep meaning to look into more carefully...)
It would be great to have the S-forms and/or Q-forms filled in. To an
extent, FSL does this.
That's why I use medcon to go to Analyze -medcon nifti would just glue
the image to the header and not fill any extra fields- and convert to
nifti with avwchfiletype. Then at least the S-form is filled in (filling
out the Q-form wit S-form information is a bit too much of a good thing
-and actually wrong- but I don't think it does any harm).
> One trick that might help though (again, I haven't looked into this) is
> to use medcon to stack the DICOM slices into a DICOM volume, and then to
> convert this DICOM volume to a NIfTI one with e.g. dcm2nii etc.
Haven't tried that!
> At one point I was using a simple command to create a DICOM volume
> medcon -f `slice_set.pl` -c dicom -stack3d
> having written a slightly more complicated Perl script, slice_set.pl, to
> pick out and order the slices (for some rather messed up "anonymised"
> DICOM data that I got, which confused all the automated series-ordering
> software). Also, if you haven't already spotted them, the "mklinks"
> scripts from the medcon FAQ are very useful
> http://xmedcon.sourceforge.net/Faq/Stack
> http://xmedcon.sourceforge.net/pub/mklinks
> http://xmedcon.sourceforge.net/pub/mklinks2
I'm not sure what they do? Looking at my nifti output (appears to be
correct) those tools are not needed here?
> You'd think that getting the data from the scanner to a form that could
> be analysed easily with FSL/SPM/etc, while preserving as much
> information as possible, would be a solved problem by now, wouldn't you?
There is surprisingly little information on what to do with a DICOM(dir)
CD!!!
cheers
Alle Meije
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