try running dcmdjpeg on it first. This will create a new set of files that
you probably want to put in another directory to avoid overwriting your raw
data
cheers
Bruce
On Fri, 16 Dec 2016, Warner, Graham Cary wrote:
Hi,
I'm trying to open a dicom using the center's instillation of freesurfer
(/usr/local/freesurfer/nmr-stable53-env) but get the following error message
when trying to load the file.
Starting DICOMRead2()
dcmfile
=/autofs/space/jazz_001/users/gwarner/mi2b2Data/1.2.124.113532.132.183.36.32
.20040903.132017.11895667/1.2.840.113619.2.25.49466.102.1094369499/1.2.840.
113619.2.25.49466.102.1.1094369499.dcm
dcmdir
=/autofs/space/jazz_001/users/gwarner/mi2b2Data/1.2.124.113532.132.183.36.32
.20040903.132017.11895667/1.2.840.113619.2.25.49466.102.1094369499
Ref Series No = 102
Found 25 files, checking for dicoms
Found 23 dicom files in series.
First Sorting
Computing Slice Direction
Vs: 0 0 6
Vs: 0 0 1
Second Sorting
Counting frames
nframes = 1
nslices = 23
ndcmfiles = 23
PE Dir = COL (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2.4.70--
ERROR: the pixel data cannot be loaded as it is JPEG compressed.
(Transfer Syntax UID: 1.2.840.10008.1.2.4.70)
jpegUID: --1.2.840.10008.1.2.4--
I am able to open the file in pydicom and even view the binary of the pixel
data but crash again when I try to use the pixel_array function. The pydicom
error also indicates that it can't handle the JSON compression. It looks
like I'm not the first person to have this
problem(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40683.html)
but the solution given here won't work for me because I can't write to the
directory mentioned.
Does anyone know another way to solve this?
Thank you,
Graham
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