Dear FreeSurfer,
When I try to use TRACULA I keep getting the following error:
mv -f /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs mv: rename /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs to /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs: No such file or directory
after entering the following command:
$ trac-all -prep -c dmrirc.preproc
I tried to specify my bval and bvec in the config file, but that doesn’t seem to help.
My data was assessed using a Siemens-scanner. Attached you can find the config-file.
Thank you in advance,
Best regards,
Robby
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the complete output can be found here:
~/Desktop/SUBJECTS_FS $ trac-all -prep -c dmrirc.preproc Badly placed ()'s. INFO: SUBJECTS_DIR is /Users/rdpauw/Desktop/SUBJECTS_FS/T1 INFO: Diffusion root is /Users/rdpauw/Desktop/SUBJECTS_FS/T1 Actual FREESURFER_HOME /Applications/freesurfer INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer Previous: /apps/gent/SL6/sandybridge/software/FreeSurfer/5.3.0-centos4_x86_64 trac-preproc -c /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/scripts/dmrirc.local -log /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/scripts/trac-all.log -cmd /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Thu Aug 21 15:59:52 CEST 2014 mri_convert /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz mri_convert /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 71 files in /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1 INFO: Scanning for Series Number 5 Scanning Directory INFO: found 65 files in series INFO: loading series header info.
RunNo = 4 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Sabbe^Linde Date and time StudyDate 20140422 StudyTime 164616.578000 SeriesTime 171854.765000 AcqTime 171832.007500 Acquisition parameters PulseSeq *ep_b0 Protocol DTI64dir_1av_b1200_2.5x2.5x2.5_sfs PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 83 InversionTime -1 RepetitionTime 10800 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 768 NImageCols 768 NFrames 65 SliceArraylSize 60 IsMosaic 1 ImgPos 961.3685 959.9193 107.7635 VolRes 2.5000 2.5000 2.5000 VolDim 96 96 60 Vc -1.0000 -0.0011 0.0062 Vr 0.0000 -0.9841 -0.1774 Vs 0.0063 -0.1774 0.9841 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: ( 96 96 60), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 10800, TR = 10800 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;
FileName /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Sabbe^Linde Date and time StudyDate 20140422 StudyTime 164616.578000 SeriesTime 171854.765000 AcqTime 171832.007500 Acquisition parameters PulseSeq *ep_b0 Protocol DTI64dir_1av_b1200_2.5x2.5x2.5_sfs PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 83 InversionTime -1 RepetitionTime 10800 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 768 NImageCols 768 NFrames 65 SliceArraylSize 60 IsMosaic 1 ImgPos 121.3850 132.3092 -36.0742 VolRes 2.5000 2.5000 2.5000 VolDim 96 96 60 Vc -1.0000 -0.0011 0.0062 Vr 0.0000 -0.9841 -0.1774 Vs 0.0063 -0.1774 0.9841 VolCenter 1.8567 0.7748 17.1866 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = 0.0062587 -0.177391 0.98412 INFO: no Siemens slice order reversal detected (good!). TR=10800.00, TE=83.00, TI=-1.00, flip angle=90.00 i_ras = (-0.99998, -0.00111026, 0.00615943) j_ras = (3.52518e-09, -0.98414, -0.177395) k_ras = (0.0062587, -0.177391, 0.98412) writing to /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz... flip4fsl /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 15.625 fslswapdim /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz x -y z /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.nii.gz mv -f /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs mv: rename /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs to /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs: No such file or directory Darwin ge24p176.ugent.be 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Thu Aug 21 16:00:45 CEST 2014
Robby De Pauw, dra. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent
Robby.DePauw@Ugent.be