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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