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

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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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