I'm trying to convert the dicom to the original 001.mgz file using the following command on a Mac OSX Yosemite version 10.10.5. My SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/ . My current working directory is /Users/csfinuf/Desktop/freesurfer/morerepeat/ . The following is the output and error that I get. I'm running the latest version v 5.3.0 of freesurfer. Any suggestions on what the problem is? What is strange that it works with half my data set but the other has this error. I've run this command in the exact way many times before and have never had this issue.
bash-3.2$ recon-all -i /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm -subjid Bigler_Repeatability_0005Ad_M1 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin NS112201PSY2.byu.edu <http://ns112201psy2.byu.edu/> 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1 \n mri_convert /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz \n mri_convert /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm... Getting Series No INFO: Found 178 files in /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1 INFO: Scanning for Series Number 2 Scanning Directory INFO: found 176 files in series INFO: loading series header info. RunNo = 1 INFO: sorting. INFO: (224 256 176), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Bigler_Repeatability_AD_M Date and time StudyDate 20160512 StudyTime 075942.531000 SeriesTime 081401.859000 AcqTime 080647.620000 Acquisition parameters PulseSeq *tfl3d1_ns Protocol t1_mpr_sag_iso_ave2_ipat2_(mprage) PhEncDir ROW EchoNo 1 FlipAngle 9 EchoTime 2.26 InversionTime 900 RepetitionTime 1900 PhEncFOV 218.75 ReadoutFOV 250 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 256 NImageCols 224 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 75.8389 136.8499 125.0000 VolRes 0.9766 0.9766 1.0000 VolDim 224 256 176 Vc 0.0767 -0.9971 0.0000 Vr -0.0000 0.0000 -1.0000 Vs -0.9971 -0.0767 0.0000 VolCenter -3.5106 21.0460 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) Segmentation fault Darwin NS112201PSY2.byu.edu <http://ns112201psy2.byu.edu/> 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 recon-all -s Bigler_Repeatability_0005Ad_M1 exited with ERRORS at Wed Jun 8 13:39:08 MDT 2016 For more details, see the log file /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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