Try copying the following linux binaries to your $FREESURFER_HOME/bin folder (make a back up of mri_convert first)

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/dcmdjpeg.fs
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/dcmdrle.fs

I've tested this on some but not a lot of data, so please let me know if it works for you
best
doug


On 11/19/15 3:38 PM, Baker, Justin T.,M.D.,Ph.D. wrote:
Hi FreeSurfer list,

Lately, we have noticed that a bunch of DICOMs obtained on our 3T Tim Trio (at McLean Hospital) are getting labeled with TransferSyntax IDs that are causing DICOM unpacking scripts (like mri_convert) to fail.  

In particular, the offending TransferSyntaxIDs appear to be "1.2.840.10008.1.2.4.90" and "1.2.840.10008.1.2.4.91", according to what we can glean from the DICOM headers.  It seems like the "JPEG Lossless Only" syntax is the real problem, but in any case, we are not finding any suitable workarounds for this issue.

Any advice on how to proceed would be much appreciated.  We are hoping that a patch to "mri_convert" would solve the problem.

Best,
Justin

  






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