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Hi FreeSurfer Developers,

I'm attempting to perform a full recon-all on the dicom/nifti file for test my freesurfer installation 
as described on the website https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall but I have an error like this;

recon-all -s file1 -i /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm -all

Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux sid 4.18.0-17-generic #18-Ubuntu SMP Wed Mar 13 14:34:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/freesurfer/subjects/file1

 mri_convert /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm /usr/local/freesurfer/subjects/file1/mri/orig/001.mgz 

mri_convert /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm /usr/local/freesurfer/subjects/file1/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm...
Starting DICOMRead2()
dcmfile = /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm
dcmdir = /home/ebru/Desktop/den01_org/T1_1
Ref Series No = 201
Found 182 files, checking for dicoms
Found 180 dicom files in series.
First Sorting
Computing Slice Direction
Vs: -0.0462818 0.24329 0.968857
Vs: -0.0462815 0.243288 0.968849
Second Sorting
Counting frames
nframes = 1
nslices = 180
ndcmfiles = 180
PE Dir = COL (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2.1--
Loading pixel data
TR=8.39, TE=3.86, TI=0.00, flip angle=8.00
i_ras = (-0.996607, -0.0773363, 0.0281873)
j_ras = (0.0680693, -0.966865, -0.246046)
k_ras = (0.0462815, -0.243288, 0.968849)
writing to /usr/local/freesurfer/subjects/file1/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Įrū Nis 24 11:45:57 +03 2019
Found 1 runs
/usr/local/freesurfer/subjects/file1/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.

 cp /usr/local/freesurfer/subjects/file1/mri/orig/001.mgz /usr/local/freesurfer/subjects/file1/mri/rawavg.mgz 

/usr/local/freesurfer/subjects/file1

 mri_convert /usr/local/freesurfer/subjects/file1/mri/rawavg.mgz /usr/local/freesurfer/subjects/file1/mri/orig.mgz --conform 

mri_convert /usr/local/freesurfer/subjects/file1/mri/rawavg.mgz /usr/local/freesurfer/subjects/file1/mri/orig.mgz --conform 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /usr/local/freesurfer/subjects/file1/mri/rawavg.mgz...
TR=8.39, TE=3.86, TI=0.00, flip angle=8.00
i_ras = (-0.996607, -0.0773363, 0.0281873)
j_ras = (0.0680693, -0.966865, -0.246046)
k_ras = (0.0462815, -0.243288, 0.968849)
Original Data has (0.976562, 0.976562, 1) mm size and (256, 256, 180) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /usr/local/freesurfer/subjects/file1/mri/orig.mgz...

 mri_add_xform_to_header -c /usr/local/freesurfer/subjects/file1/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/file1/mri/orig.mgz /usr/local/freesurfer/subjects/file1/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Įrū Nis 24 11:46:09 +03 2019
/usr/local/freesurfer/subjects/file1/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz 

Linux sid 4.18.0-17-generic #18-Ubuntu SMP Wed Mar 13 14:34:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s file1 exited with ERRORS at Įrū Nis 24 11:46:11 +03 2019

For more details, see the log file /usr/local/freesurfer/subjects/file1/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

I've searched the list and no similar errors have been reported. 
Does anyone have any thoughts on how to trouble-shoot this one?

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) Ubuntu version:18.10
3) uname -a: Linux sid 4.18.0-17-generic #18-Ubuntu SMP Wed Mar 13 14:34:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached