Hi,
here is a (not so polished) list of converters and DICOM header
parsers, along with my personal experience with those tools.
The structure of the list is as follows:
url
purpose of the program
name of the program
my personal experience
http://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert
converter
mri_convert: good. must pick random file from series, will
automatically find the remaining files
http://www.cabiatl.com/mricro/mricron/dcm2nii.html
converter
dcm2nii
buggy
segfault when src path ends with '/'
does sometimes not read the orientation, slice
thickness or pixel spacing correctly, and does not allow for
correction on the command line or elsewhere
does NOT issue a warning that some values could
not be read from the header, which can result in left/right flips
reads default values from config file, which are
overwritten by command line
one can not choose the output filename, one can only
choose between some predefined sprintf strings
overview on bottom
http://godzilla.kennedykrieger.org/dicomfiles/
converter
dcm_convert: Philips ACS/NT (not yet tested)
solaris binary only
overview
http://cbi.nyu.edu/software/dinifti.php
converter
dinifti
based on ctn, ctn is very good
has man pages
is not able to read number of slices, allows for correction
can not read orientation
source code looks unstable (c strtok, round from float to
integer to determine number of slices)
http://erl.wustl.edu/research/dicom/ctn.html
header
dcm_dump_file: (very good)
dicomhead: (could not read anything)
dcmtk
header
dcmdump: (works)
libgdcm-tools
header
gdcmdump
converter
gdcmconv: (dcm -> dcm)
http://lcni.uoregon.edu/~jolinda/MRIConvert/
converter
mcverter
segfaulted
MRIconvert (gui)
http://xmedcon.sourceforge.net
converter nifti -> dicom
medcon: cli
xmedcon: gui
works for nifti -> dicom
dicom -> nifti untested
http://www.loni.ucla.edu/Software/Debabeler
converter
debabeler
can not read time series, concatenates all volumes in the
z direction (see views->dicom 2 nifti translation->image dimensions)
sets all dimensions starting with pixdim5 to zero, which
causes fslview to exit with a failing assertion (would expect 1
instead of 0)
oro.dicom, oro.nifti
ezDICOM
Cheers,
Klaus
On Tue, Sep 25, 2012 at 8:05 PM, Chuck Theobald <[log in to unmask]> wrote:
> Hello Basile,
>
> You could try MRIConvert: http://lcni.uoregon.edu/~jolinda/MRIConvert/
>
> We respond to support queries and code often, even in the midst of a move
> across campus to a new Center. Note that the package comes with a
> command-line program, mcverter, to support scripted processing pipelines.
>
> Regards,
> Chuck
>
>
>
> On 9/25/12 8:45 AM, Basile Pinsard wrote:
>>
>> Dear all
>>
>> I post here questions about dcm2nii because this sofware despite it's
>> widespread use does not have any kind of support (no list/no working email
>> address...).
>> There seems to be regular updates and it's working but the documentation
>> is not updated and options that have been listed on the webpage are not
>> functional such as BeginClip and LastClip or UINT16toFLOAT32 and a lots of
>> the options added by default in dcm2nii.ini are not documented.
>>
>> How many of you are using it in "production", how do you deal with this
>> limited support?
>> Are there any other good alternatives for fmri dicom to nifti conversion
>> that work on all constructors data?
>>
>> Thanks for your thought about what I consider to be a problem in the
>> development of reliable and maintainable processing pipelines.
>>
>> Regards.
>>
>
>
> --
> Chuck Theobald
> System Administrator
> The Robert and Beverly Lewis Center for Neuroimaging
> University of Oregon
> P: 541-346-0343
> F: 541-346-0345
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