External Email - Use Caution
Hello:
I have a problem when running trac-all preprocessing. I have X11 and FSL
installed. Not Matlab I don’t know if I need it I think only for fMRI.
Sincerely,
Andrade.
Renes-MacBook-Air-2:diffusion_tutorial andraderenew$ 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
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 Wed Jul 11 17:53:23 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
Traceback (most recent call last):
File "/usr/local/fsl/bin/imglob", line 11, in <module>
load_entry_point('fslpy==1.7.0', 'console_scripts', 'imglob')()
File
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/fsl/scripts/imglob.py",
line 109, in main
print(' '.join(imgfiles))
UnicodeEncodeError: 'ascii' codec can't encode character '\u0301' in position
32: ordinal not in range(128)
Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in
seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final
option value
mv -f
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvecs
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvecs.norot
xfmrot
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvecs.norot
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvecs
grep:
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog:
No such file or directory
head:
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog:
No such file or directory
wc:
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog:
open: No such file or directory
wc:
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog:
open: No such file or directory
ERROR: Transform file should be eddy_correct/eddy log file or .mat file
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 Wed Jul 11 17:55:25 CEST 2018_______________________________________________
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