matlab's dicomread can handle 8 bit images, so if you have matlab, one could write a script to convert your dicoms to mgh format (using save_mgh).

> Date: Fri, 30 Jan 2009 16:06:52 -0500
> From: greve@nmr.mgh.harvard.edu
> To: senumah@fas.harvard.edu
> Subject: Re: [Freesurfer] difficulty readings DICOM files from CD
> CC: freesurfer@nmr.mgh.harvard.edu
>
>
> This might not work with our tools. As the message implies, they cannot
> unpack 8bit images (I think it is fixed at 16). I'm not sure how to
> change it (or if it can be changed). We use a 3rd party dicom reader,
> and it is not an easy thing modify.
>
> sorry
>
> doug
>
> Sam Enumah wrote:
> >
> > Hello,
> >
> > My name is Sam Enumah and I am an undergraduate working in the A.A.
> > Martinos Imaging Center at MGH Navy Yard. I have become familiar with
> > Freesurfer's tkmedit function and I am able to analyze my data once I
> > am given a set of 144 MR dicom files. While the mri_convert tool
> > works for the dicom files that are on the local machine, I cannot seem
> > to get it to work for the files I have tried to retrieve from a CD.
> > The files on my local host machine all display the extension ".dcm"
> > while the files from the CD do not display a file extension and are
> > files with names that consist of 8 unique numbers (e.g 48480095)
> >
> > As you may know, when running mri_convert, the user need only input
> > one of the files in a series and it recognizes all the other files and
> > creates the desired output (in this case the ".nii" file type to be
> > read by tkmedit). However, when I tried to input these 8 digit file
> > names into mri_convert, I received the following error:
> >
> > [gordo:12250000] (nmr-std-env) mri_convert 48480995.dcm adc.nii
> > mri_convert 48480995.dcm adc.nii
> > $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $
> > reading from 48480995.dcm...
> > Starting DICOMRead2()
> > dcmfile = /autofs/homes/014/xmlentz/
> > Desktop/dicom/08110217/12250000/48480995.dcmdcmdir =
> > /autofs/homes/014/xmlentz/Desktop/dicom/08110217/12250000
> > Ref Series No = 805
> > ERROR: bits = 8 not supported.
> > Send email to freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>
> >
> > I tried
> > "mri_convert <filename> --in_type ge adc.nii"
> > but kept getting the error:
> > genesisRead(): can't determine file name format
> >
> > Essentially, my problem is that I have roughly 1000 dicom files (as
> > evidenced by command "file" in terminal) without an identifiable
> > extension and I need to find a way to change these into one of any of
> > the set MR001.dcm - MR144.dcm to be read by mri_convert.
> >
> > As it stands now, I don't know what series (average DC, isotropic, FA,
> > etc.) these 8 digit numbers correspond to so I'm unsure of how to proceed.
> > Suggestions?
> >
> > Thanks for your time.
> >
> > -Sam
> >
> > --
> > Sam Enumah
> > Harvard College Class of 2010
> > Concentrator in Neurobiology
> > senumah@fas.harvard.edu <mailto:senumah@fas.harvard.edu>
> > ------------------------------------------------------------------------
> >
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> > Freesurfer@nmr.mgh.harvard.edu
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>
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