Hi Jim,
What is in .out file? Does fsdcmdecompress work if you submit it manually at the prompt?
Can you also try the following?
1. setting environment variable FS_DCM_DECOMPRESS setenv FS_DCM_DECOMPRESS DCMTK if you are using bash, use 'export FS_DCM_DECOMPRESS=DCMTK' 2. submit recon-all
Let me know if it works.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Wednesday, January 18, 2023 2:37 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Kenley, Jeanette jkkenley@wustl.edu Subject: [Freesurfer] dicom reading errors
External Email - Use Caution Trying to run FS7.2. on a dataset and am getting dicom errors as shown below. Looks like some issues related to dicom compression and bad fd number.
Any suggestions from the FS experts please? Jim
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