Eddy correct command not found - Freesurfer

29 Jun 2018


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Dear community:
I have a problem with trac-all processing with the tutorial data.
sh-3.2# trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial
INFO: SUBJECTS_DIR is /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_recons
INFO: Diffusion root is /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial
Actual FREESURFER_HOME /Applications/freesurfer
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20130423
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
flirt: Command not found.
INFO: current FREESURFER_HOME does not match that of previous processing.
    Current: /Applications/freesurfer
    Previous: /usr/local/freesurfer/dev
trac-preproc -c /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/dmrirc.local -log /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/trac-all.log -cmd /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/trac-all.cmd
#-------------------------------------
/Applications/freesurfer/bin/trac-preproc 
#-------------------------------------
#@# Image corrections Fri Jun 29 21:19:12 CEST 2018
mri_convert --bvec-voxel /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm...
Getting Series No 
INFO: Found 75 files in /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig
INFO: Scanning for Series Number 11
Scanning Directory 
INFO: found 70 files in series
INFO: loading series header info.
RunNo = 10
WARNING: Run 1 appears to be truncated
  Files Found: 70, Files Expected (lRep+1): 120
FileName 		/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
Identification
    NumarisVer        syngo MR 2004A 4VA25A 
    ScannerModel      Trio
    PatientName       Trio_calib_002_run2 
Date and time
    StudyDate         20050905
    StudyTime         100821.656000 
    SeriesTime        104226.748000 
    AcqTime           104209.522496 
Acquisition parameters
    PulseSeq          ep_b0#0 
    Protocol          DIFFUSION_HighRes 
    PhEncDir          COL
    EchoNo            0
    FlipAngle         90
    EchoTime          100
    InversionTime     -1
    RepetitionTime    10100
    PhEncFOV          256
    ReadoutFOV        256
Image information
    RunNo             10
    SeriesNo          11
    ImageNo           1
    NImageRows        1024
    NImageCols        1024
    NFrames           70
    SliceArraylSize   60
    IsMosaic          1
    ImgPos            1048.1801 1002.6923 -265.4914 
    VolRes              2.0000   2.0000   2.0000 
    VolDim            128      128       60 
    Vc                 -0.9997   0.0244   0.0005 
    Vr                 -0.0238  -0.9764   0.2147 
    Vs                  0.0057   0.2147   0.9767 
    VolCenter           0.0000   0.0000   0.0000 
    TransferSyntaxUID unknown
INFO: sorting.
INFO: (128 128  60), nframes = 70, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Numaris Version: syngo MR 2004A 4VA25A  Maj = 4, Min=2, MinMin = 5 
Repetition Time = 10100, TR = 10100 ms
PE Dir COL COL
AutoAlign matrix detected 
AutoAlign Matrix --------------------- 
 0.99970   0.02376  -0.00570  -0.49480;
-0.02443   0.97638  -0.21466  -40.55519;
 0.00047   0.21474   0.97667   12.50291;
 0.00000   0.00000   0.00000   1.00000;
FileName 		/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
Identification
    NumarisVer        syngo MR 2004A 4VA25A 
    ScannerModel      Trio
    PatientName       Trio_calib_002_run2 
Date and time
    StudyDate         20050905
    StudyTime         100821.656000 
    SeriesTime        104226.748000 
    AcqTime           104209.522496 
Acquisition parameters
    PulseSeq          ep_b0#0 
    Protocol          DIFFUSION_HighRes 
    PhEncDir          COL
    EchoNo            0
    FlipAngle         90
    EchoTime          100
    InversionTime     -1
    RepetitionTime    10100
    PhEncFOV          256
    ReadoutFOV        256
Image information
    RunNo             10
    SeriesNo          11
    ImageNo           1
    NImageRows        1024
    NImageCols        1024
    NFrames           70
    SliceArraylSize   60
    IsMosaic          1
    ImgPos            131.1612 149.7402 -72.6670 
    VolRes              2.0000   2.0000   2.0000 
    VolDim            128      128       60 
    Vc                 -0.9997   0.0244   0.0005 
    Vr                 -0.0238  -0.9764   0.2147 
    Vs                  0.0057   0.2147   0.9767 
    VolCenter           0.5005  40.7699  13.4796 
    TransferSyntaxUID unknown
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 0
sagrev = 1, correv =1, trarev = 0
Vs = 0.0057 0.214665 0.976671
INFO: no Siemens slice order reversal detected (good!). 
TR=10100.00, TE=100.00, TI=-1.00, flip angle=90.00
i_ras = (-0.999702, 0.0244268, 0.000465598)
j_ras = (-0.023757, -0.976382, 0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
writing to /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz...
mri_probedicom --i /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dcminfo.dat
cp /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/gradients.txt /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs
cp /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/bvalues.txt /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals
mv -f /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvecs.tmp /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs
mv -f /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvals.tmp /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals
orientLAS /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 8
mri_convert -oni 128 -onj 128 -onk 60 -oid -0.999701 0.0244268 0.000465598 -ojd 0.023757 0.976382 -0.21474 -okd 0.0057 0.214665 0.976671 -oc 0.548018 42.7227 13.0501 -rt nearest /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 128 -onj 128 -onk 60 -oid -0.999701 0.0244268 0.000465598 -ojd 0.023757 0.976382 -0.21474 -okd 0.0057 0.214665 0.976671 -oc 0.548018 42.7227 13.0501 -rt nearest /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz 
normalizing out_i_direction: (-0.999701, 0.0244268, 0.000465598) -> (-0.999702, 0.0244268, 0.000465598)
normalizing out_j_direction: (0.023757, 0.976382, -0.21474) -> (0.023757, 0.976382, -0.21474)
normalizing out_k_direction: (0.0057, 0.214665, 0.976671) -> (0.0057, 0.214665, 0.976671)
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz...
TR=10100.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999701, 0.0244268, 0.000465598)
j_ras = (-0.023757, -0.976382, 0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
Reslicing using nearest 
writing to /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz...
INFO: found /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals, copying
INFO: found /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs, converting to LAS
mv -f /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.bvecs /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvecs
mv -f /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.bvals /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvals
eddy_correct /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz 0
eddy_correct: Command not found.
Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Fri Jun 29 21:20:22 CEST 2018
What should be the problem?
Sincerely, 
Andrade.