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