Hi, Thank you a lot! It now ran, but exited with errors: ERROR: fMRIframe: frame >= n frames Can you help me? Regards, Pedro Rosa
[server:~/Desktop] pedrogomesrosa% trac-all -corr -c config INFO: SUBJECTS_DIR is /Users/pedrogomesrosa/Desktop INFO: Diffusion root is /Users/pedrogomesrosa/Desktop Actual FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/Freesurfer5.3/freesurfer Previous: /Volumes/Data/Freesurfer_5.3/freesurfer trac-preproc -c /Users/pedrogomesrosa/Desktop/ESNA148/scripts/dmrirc.local -log /Users/pedrogomesrosa/Desktop/ESNA148/scripts/trac-all.log -cmd /Users/pedrogomesrosa/Desktop/ESNA148/scripts/trac-all.cmd #------------------------------------- /Applications/Freesurfer5.3/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fri May 16 08:35:20 BRT 2014 mri_convert /Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808371376939956.dcm /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.nii.gz mri_convert /Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808371376939956.dcm /Users/pedrogomesrosa/Desktop/ESNA148/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/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808371376939956.dcm... Getting Series No INFO: Found 6612 files in /Users/pedrogomesrosa/Desktop//148 INFO: Scanning for Series Number 5 Scanning Directory INFO: found 6501 files in series INFO: loading series header info. error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/strings: can't open file: /Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808391678947142928 (No such file or directory) error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/strings: can't open file: copy.dcm (No such file or directory)
RunNo = 4 WARNING: Run 4 appears to be truncated Slice = 1, nthframe = 1, nframes = 2, 0 INFO: sorting. INFO: (120 120 1), nframes = 2, ismosaic=0 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;
ERROR: nlist (6501) > nslices (1) x frames (2) ERROR: dump file list into fileinfo.txt. ERROR: check for consistency ERROR: set nlist = nslices*nframes. FileName /Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808214939782717907.dcm Identification NumarisVer syngo MR B15 ScannerModel Espree PatientName RODRIGUES^ADRIANA C Date and time StudyDate 20121128 StudyTime 075625.593000 SeriesTime 082207.781000 AcqTime 082147.882500 Acquisition parameters PulseSeq *ep_b0 Protocol DIF 64 2NEX 2.7mmX2mm Trigger (Ax Puro) PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 110 InversionTime -1 RepetitionTime 8000 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 120 NImageCols 120 NFrames 2 SliceArraylSize 50 IsMosaic 0 ImgPos 120.1304 78.5600 -52.6158 VolRes 2.0000 2.0000 2.7000 VolDim 120 120 1 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.1304 -41.4400 -51.2658 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=8000.00, TE=110.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.nii.gz... mri_probedicom --i /Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808371376939956.dcm > /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dcminfo.dat cp /Users/pedrogomesrosa/Desktop/bvec.bvec /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.mghdti.bvecs cp /Users/pedrogomesrosa/Desktop/bval.bval /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.mghdti.bvals mv -f /Users/pedrogomesrosa/Desktop/ESNA148/dmri/bvecs.tmp /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.mghdti.bvecs mv -f /Users/pedrogomesrosa/Desktop/ESNA148/dmri/bvals.tmp /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.mghdti.bvals flip4fsl /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.nii.gz /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 10.8 fslswapdim /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.nii.gz x -y z /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig_flip.nii.gz INFO: found /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig_flip.mghdti.bvecs /Users/pedrogomesrosa/Desktop/ESNA148/dmri/bvecs mv -f /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig_flip.mghdti.bvals /Users/pedrogomesrosa/Desktop/ESNA148/dmri/bvals mv -f /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig_flip.nii.gz /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi.nii.gz ln -sf /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi.nii.gz /Users/pedrogomesrosa/Desktop/ESNA148/dmri/data.nii.gz mri_convert --frame 0 /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi.nii.gz /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi.nii.gz /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi.nii.gz... TR=8000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_frame0.nii.gz... mri_convert --frame 65 /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi.nii.gz /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_frame65.nii.gz mri_convert --frame 65 /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi.nii.gz /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_frame65.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi.nii.gz... TR=8000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) keeping frame 65 ERROR: fMRIframe: frame >= nframes Darwin server.macbookpro.com 13.1.0 Darwin Kernel Version 13.1.0: Wed Apr 2 23:52:02 PDT 2014; root:xnu-2422.92.1~2/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Fri May 16 08:38:39 BRT 2014
On Friday, May 16, 2014 at 8:20 AM, ayendiki@nmr.mgh.harvard.edu wrote:
Hi Pedro - Your config file needs to be a plain text file, not a rich text format (rtf) file. If you run the cat command on your file, you'll see that there are some formatting strings that were added by your text editor in the beginning of the file and they include the curly brackets that give you the error.
Hope this helps, a.y
Dear all, I am facing an error at the configuration file for trac-all I am trying to run a single subject, 148, for who there is a folder ‘148’ with all DWI DICOMs and a folder ‘ESNA148’ with the recon-all processing (Freesurfer 5.3). Also in $SUBJECTS_DIR there is bval.bval and bvec.bvec. I attached the configuration file. However, I am facing the following error, although no run list is specified: [server:~/Desktop] pedrogomesrosa% trac-all -corr -c config.rtf Missing }. Missing }. }: Command not found. Missing }. red255green255blue255: Command not found. red240green242blue245: Command not found. }: Command not found. margl1440margr1440vieww22600viewh9020viewkind0: Command not found. deftab720: Command not found. pardpardeftab720: Command not found. ERROR: run list is longer than subject list
Any input is appreciated. Regards, Pedro Rosa.
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