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: gr...@nmr.mgh.harvard.edu > To: senu...@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 > > senu...@fas.harvard.edu <mailto:senu...@fas.harvard.edu> > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _________________________________________________________________ Hotmail® goes where you go. On a PC, on the Web, on your phone. http://www.windowslive-hotmail.com/learnmore/versatility.aspx#mobile?ocid=TXT_TAGHM_WL_HM_versatility_121208
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