Hello, Freesurfer experts:

I followed the tutorial for FStutorial/diffusion: 

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion

surfer.nmr.mgh.harvard.edu
The purpose of this tutorial is to give you experience with the integration of Diffusion Tensor Imaging (DTI) with FreeSurfer. The data were collected at MGH as part ...
And i export the variables and run the command dt_recon both on my MAC and Ubuntu for the tutorial subject which located in:  

TUTORIAL_DIR=$TUTORIAL_DATA/diffusion_tutorial/Diff001
Just to be sure, So I run it on both systems, and I got the same errors:


dt_recon --i /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm --s Diff001 --o /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon
INFO: SUBJECTS_DIR is /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_recons
dt_recon logfile
Wed Dec 21 15:13:51 CET 2016
VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $
setenv SUBJECTS_DIR /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_recons
cd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion
/Applications/freesurfer/bin/dt_recon --i /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm --s Diff001 --o /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon
UMR-COGIM-MP008
junhao.wen
/usr/local/fsl/bin/eddy_correct
ECRefTP 0
#@#-------------------------------
Converting input
Wed Dec 21 15:13:51 CET 2016
cd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion
mri_convert /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi.nii
mri_convert /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm...
Getting Series No
INFO: Found 3 files in /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig
INFO: Scanning for Series Number 6
Scanning Directory
INFO: found 1 files in series
INFO: loading series header info.

RunNo = 5
WARNING: Run 1 appears to be truncated
  Files Found: 1, Files Expected (lRep+1): 120
FileName /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm
Identification
NumarisVer        syngo MR 2002B 4VA21A
ScannerModel      Sonata
PatientName       anon
Date and time
StudyDate         00000000
StudyTime         110208.000000
SeriesTime        114533.812000
AcqTime           114020.732488
Acquisition parameters
PulseSeq          ep_b0#0
Protocol          DIFFUSION_HighRes_auto
PhEncDir          COL
EchoNo            0
FlipAngle         90
EchoTime          80
InversionTime     -1
RepetitionTime    8900
PhEncFOV          256
ReadoutFOV        256
Image information
RunNo             5
SeriesNo          6
ImageNo           1
NImageRows        1024
NImageCols        1024
NFrames           1
SliceArraylSize   64
IsMosaic          1
ImgPos            958.4660 1120.5343 -85.7814
VolRes              2.0000   2.0000   2.0000
VolDim            128      128       64
Vc                 -0.9981  -0.0596  -0.0171
Vr                  0.0588  -0.9972   0.0460
Vs                 -0.0198   0.0449   0.9988
VolCenter           0.0000   0.0000   0.0000
TransferSyntaxUID 1.2.840.10008.1.2
INFO: sorting.
INFO: (128 128  64), nframes = 1, ismosaic=1
Numaris Version: syngo MR 2002B 4VA21A  Maj = 4, Min=2, MinMin = 1
Repetition Time = 8900, TR = 8900 ms
PE Dir COL COL
This looks like an MGH DTI volume
MGH DTI SeqPack Info
0 ep_b0#0  0.000000 0
bValue = 700
nB0 = 10
nDir = 60
GradFile /Applications/freesurfer/diffusion/mgh-dti-seqpack/gradient_mgh_dti60.gdt
FileName /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm
Identification
NumarisVer        syngo MR 2002B 4VA21A
ScannerModel      Sonata
PatientName       anon
Date and time
StudyDate         00000000
StudyTime         110208.000000
SeriesTime        114533.812000
AcqTime           114020.732488
Acquisition parameters
PulseSeq          ep_b0#0
Protocol          DIFFUSION_HighRes_auto
PhEncDir          COL
EchoNo            0
FlipAngle         90
EchoTime          80
InversionTime     -1
RepetitionTime    8900
PhEncFOV          256
ReadoutFOV        256
Image information
RunNo             5
SeriesNo          6
ImageNo           1
NImageRows        1024
NImageCols        1024
NFrames           1
SliceArraylSize   64
IsMosaic          1
ImgPos            116.8592 173.6140 -59.8600
VolRes              2.0000   2.0000   2.0000
VolDim            128      128       64
Vc                 -0.9981  -0.0596  -0.0171
Vr                  0.0588  -0.9972   0.0460
Vs                 -0.0198   0.0449   0.9988
VolCenter          -4.6346  41.2132   7.7661
TransferSyntaxUID 1.2.840.10008.1.2
UseSliceScaleFactor 0 (slice 0: 1)
sagrev = 0, correv =0, trarev = 0
Vs = -0.0197543 0.0448988 0.998796
INFO: no Siemens slice order reversal detected (good!).
TR=8900.00, TE=80.00, TI=-1.00, flip angle=90.00
i_ras = (-0.998075, -0.0596198, -0.0170599)
j_ras = (0.0587821, -0.997211, 0.0459901)
k_ras = (-0.0197543, 0.0448988, 0.998796)
writing to /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi.nii...
Saving bvals and bvecs


cd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion
mri_probedicom --i /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm


#@#-------------------------------
Eddy/Motion Correct
Wed Dec 21 15:13:52 CET 2016
cd /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/ectmp
eddy_correct /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi.nii /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii 0
processing /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec_tmp0000


#@#-------------------------------
Fitting Tensors
Wed Dec 21 15:14:05 CET 2016
cd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion
mri_glmfit --y /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii --glmdir /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon --dti /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-infodump.dat

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion
cmdline mri_glmfit --y /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii --glmdir /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon --dti /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-infodump.dat
sysname  Darwin
hostname UMR-COGIM-MP008
machine  x86_64
user     junhao.wen
FixVertexAreaFlag = 1
UseMaskWithSmoothing     1
OneSampleGroupMean 0
y    /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii
logyflag 1
X    /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-infodump.dat
usedti  1
glmdir /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon
Loading y from /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii
Using DTI
bValue = 700
nB0 = 10
nDir = 60
GradFile /Applications/freesurfer/diffusion/mgh-dti-seqpack/gradient_mgh_dti60.gdt
Saving design matrix to /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/Xg.dat
Normalized matrix condition is 27.8243
Matrix condition is 979968
Pruning voxels by thr: 50.000000
Found 961982 voxels in mask
Saving mask to /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/mask.nii
search space = 7695856.000000
ERROR: dimension mismatch between y and X.
  y has 1 inputs, X has 70 rows.
 ✘  ~/Hao/tutorial/Freesurfer/diffusion  export TUTORIAL_DIR=/Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial
 ~/Hao/tutorial/Freesurfer/diffusion  export SUBJECTS_DIR=/Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_recons
 ~/Hao/tutorial/Freesurfer/diffusion  dt_recon --i $TUTORIAL_DIR/$subj/orig/*-1.dcm --s $subj --o $TUTORIAL_DIR/$subj/dtrecon
zsh: no matches found: /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial//orig/*-1.dcm
 ✘  ~/Hao/tutorial/Freesurfer/diffusion  subj=Diff001
 ~/Hao/tutorial/Freesurfer/diffusion  dt_recon --i $TUTORIAL_DIR/$subj/orig/*-1.dcm --s $subj --o $TUTORIAL_DIR/$subj/dtrecon
INFO: SUBJECTS_DIR is /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_recons
dt_recon logfile
Wed Dec 21 15:18:49 CET 2016
VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $
setenv SUBJECTS_DIR /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_recons
cd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion
/Applications/freesurfer/bin/dt_recon --i /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm --s Diff001 --o /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon
UMR-COGIM-MP008
junhao.wen
/usr/local/fsl/bin/eddy_correct
ECRefTP 0
#@#-------------------------------
Converting input
Wed Dec 21 15:18:49 CET 2016
cd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion
mri_convert /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi.nii
mri_convert /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm...
Getting Series No
INFO: Found 3 files in /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig
INFO: Scanning for Series Number 6
Scanning Directory
INFO: found 1 files in series
INFO: loading series header info.

RunNo = 5
WARNING: Run 1 appears to be truncated
  Files Found: 1, Files Expected (lRep+1): 120
FileName /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm
Identification
NumarisVer        syngo MR 2002B 4VA21A
ScannerModel      Sonata
PatientName       anon
Date and time
StudyDate         00000000
StudyTime         110208.000000
SeriesTime        114533.812000
AcqTime           114020.732488
Acquisition parameters
PulseSeq          ep_b0#0
Protocol          DIFFUSION_HighRes_auto
PhEncDir          COL
EchoNo            0
FlipAngle         90
EchoTime          80
InversionTime     -1
RepetitionTime    8900
PhEncFOV          256
ReadoutFOV        256
Image information
RunNo             5
SeriesNo          6
ImageNo           1
NImageRows        1024
NImageCols        1024
NFrames           1
SliceArraylSize   64
IsMosaic          1
ImgPos            958.4660 1120.5343 -85.7814
VolRes              2.0000   2.0000   2.0000
VolDim            128      128       64
Vc                 -0.9981  -0.0596  -0.0171
Vr                  0.0588  -0.9972   0.0460
Vs                 -0.0198   0.0449   0.9988
VolCenter           0.0000   0.0000   0.0000
TransferSyntaxUID 1.2.840.10008.1.2
INFO: sorting.
INFO: (128 128  64), nframes = 1, ismosaic=1
Numaris Version: syngo MR 2002B 4VA21A  Maj = 4, Min=2, MinMin = 1
Repetition Time = 8900, TR = 8900 ms
PE Dir COL COL
This looks like an MGH DTI volume
MGH DTI SeqPack Info
0 ep_b0#0  0.000000 0
bValue = 700
nB0 = 10
nDir = 60
GradFile /Applications/freesurfer/diffusion/mgh-dti-seqpack/gradient_mgh_dti60.gdt
FileName /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm
Identification
NumarisVer        syngo MR 2002B 4VA21A
ScannerModel      Sonata
PatientName       anon
Date and time
StudyDate         00000000
StudyTime         110208.000000
SeriesTime        114533.812000
AcqTime           114020.732488
Acquisition parameters
PulseSeq          ep_b0#0
Protocol          DIFFUSION_HighRes_auto
PhEncDir          COL
EchoNo            0
FlipAngle         90
EchoTime          80
InversionTime     -1
RepetitionTime    8900
PhEncFOV          256
ReadoutFOV        256
Image information
RunNo             5
SeriesNo          6
ImageNo           1
NImageRows        1024
NImageCols        1024
NFrames           1
SliceArraylSize   64
IsMosaic          1
ImgPos            116.8592 173.6140 -59.8600
VolRes              2.0000   2.0000   2.0000
VolDim            128      128       64
Vc                 -0.9981  -0.0596  -0.0171
Vr                  0.0588  -0.9972   0.0460
Vs                 -0.0198   0.0449   0.9988
VolCenter          -4.6346  41.2132   7.7661
TransferSyntaxUID 1.2.840.10008.1.2
UseSliceScaleFactor 0 (slice 0: 1)
sagrev = 0, correv =0, trarev = 0
Vs = -0.0197543 0.0448988 0.998796
INFO: no Siemens slice order reversal detected (good!).
TR=8900.00, TE=80.00, TI=-1.00, flip angle=90.00
i_ras = (-0.998075, -0.0596198, -0.0170599)
j_ras = (0.0587821, -0.997211, 0.0459901)
k_ras = (-0.0197543, 0.0448988, 0.998796)
writing to /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi.nii...
Saving bvals and bvecs


cd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion
mri_probedicom --i /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/orig/6-1.dcm


#@#-------------------------------
Eddy/Motion Correct
Wed Dec 21 15:18:50 CET 2016
cd /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/ectmp
eddy_correct /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi.nii /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii 0
processing /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec_tmp0000


#@#-------------------------------
Fitting Tensors
Wed Dec 21 15:19:02 CET 2016
cd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion
mri_glmfit --y /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii --glmdir /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon --dti /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-infodump.dat

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /Users/junhao.wen/Hao/tutorial/Freesurfer/diffusion
cmdline mri_glmfit --y /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii --glmdir /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon --dti /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-infodump.dat
sysname  Darwin
hostname UMR-COGIM-MP008
machine  x86_64
user     junhao.wen
FixVertexAreaFlag = 1
UseMaskWithSmoothing     1
OneSampleGroupMean 0
y    /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii
logyflag 1
X    /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-infodump.dat
usedti  1
glmdir /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon
Loading y from /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/dwi-ec.nii
Using DTI
bValue = 700
nB0 = 10
nDir = 60
GradFile /Applications/freesurfer/diffusion/mgh-dti-seqpack/gradient_mgh_dti60.gdt
Saving design matrix to /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/Xg.dat
Normalized matrix condition is 27.8243
Matrix condition is 979968
Pruning voxels by thr: 50.000000
Found 961982 voxels in mask
Saving mask to /Users/junhao.wen/Hao/Dataset/Freesurfer/FS_tutorial_data/diffusion_tutorial/Diff001/dtrecon/mask.nii
search space = 7695856.000000
ERROR: dimension mismatch between y and X.
  y has 1 inputs, X has 70 rows.

I think the problem is from fitting tensor, so do you think it is the problems of you tutorial data, I know you are going to release the new version, but anyway, this should be work, no? 


Freesurfer version 5,3,0


Thanks in advance