[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 textformat (rtf) file. If you run the cat command on your file, you'll seethat there are some formatting strings that were added by your text editorin the beginning of the file and they include the curly brackets that giveyou the error.Hope this helps,a.yDear all,I am facing an error at the configuration file for trac-allI am trying to run a single subject, 148, for who there is a folder‘148’ with all DWI DICOMs and a folder ‘ESNA148’ with therecon-all processing (Freesurfer 5.3). Also in $SUBJECTS_DIR there isbval.bval and bvec.bvec.I attached the configuration file.However, I am facing the following error, although no run list isspecified:[server:~/Desktop] pedrogomesrosa% trac-all -corr -c config.rtfMissing }.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 listAny input is appreciated.Regards,Pedro Rosa._______________________________________________Freesurfer mailing list_______________________________________________Freesurfer mailing listThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.