Did you only replace mri_convert? If so, that should not have affected mri_parse_sdcmdir. Can you restore the original mri_convert and see if the mri_parse_sdcmdir problem goes away?

On 01/15/2016 10:54 AM, Hunter Johndro wrote:

Hi All,

Currently running freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

We replaced our mri_convert function in freesurfer/bin/ with the new mri_convert function that was patched to appropriately handle 16bit SMS/Multiband sequences (the patch intended to fix errors related to the SMS-BOLD voxel intensity ranges). After swapping our mri_convert functions, unpacksdcmdir now freezes when executing mri_parse_sdcmdir (see output below). Unpacksdcmdir previously worked with this same dataset, so the mri_parse_sdcmdir error appears to be specific to the new patched mri_convert file. Any thoughts are greatly appreciated. Thanks very much!

• Hunter

Error output:

Log File is unpack//unpack.log INFO: Logfile is unpack//unpack.log SkipMoCo 0 Scanning source directory ... INFO: summary file is unpack//dicomdir.sumfile INFO: status file is unpack//parse.status Scanning directory Wed Jan 13 14:20:01 EST 2016 mri_parse_sdcmdir --sortbyrun --d raw/ --o unpack//dicomdir.sumfile --status unpack//parse.status 0

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