Hi freesurfer experts,

 

I have recently begun to use freesurfer to do structural MRI analyses.  I have been able to successfully process about 40 structural scans with recon-all thus far, but starting a few days ago, I started getting this error whenever I run recon-all:

 

WARNING: file /Users/alojos/Applications/freesurfer/subjects/sub_9999.dcm does not contain a Siemens ASCII header

has this file been anonymized?

ERROR: cannot unpack mosiacs without ASCII header

Darwin nerc130622.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64

 

recon-all -s sub_9999 exited with ERRORS at Mon May 16 08:43:24 CDT 2016

 

Here are a few of the troubleshooting steps I’ve tried to track down the cause of the error:

-     - Re-run recon-all with a couple of scans from my dataset that I have already successfully processed

-     - Re-run recon-all the same datasets but on a different computer

-     - Re-convert the scans from .ima files to dicoms in osirix, then run recon-all


For all of these steps, I have gotten the exact same error message.  The files should be anonymized, since I used osirix’s “anonymize and convert” function to generate the dicom files (the scans were given to me as .ima files).

 

Any suggestions on what to try next?

 

Thank you!
Joseph Aloi

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