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