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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