Hi Y'all,
I have not been following this thread very closely, but I just wanted to
suggest using FreeSurfer's mri_convert (if these are siemens or ge
dicoms), something like:
mri_convert onedicomfile out.nii
mri_convert onedicomfile out.nii.gz
From the one dicom file it finds the rest in the series, sorts them
properly in time and space (regardless of how they are named), and fills
in the q and s forms with the scanner coordinate transformations.
doug
Alle Meije Wink wrote:
> 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
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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