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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