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>
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