Hi, I do the pre-processing with the following command:
trac-all -prep -c ./scripts/dmrirc_single_subject THe process exits with error when it comes to fslroi (attached pls find the log file). I try to re-run the fslroi command as follow: fslroi /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi.nii. gz /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz 0 25 It works and the lowb.nii.gz looks normal. In case if I have the same problem with another dataset, how can I incorporate the number of frames (25) in the trac-all command for the fslroi? Can I continue the remaining procedures of trac-all from this point? Thank you. Phoebe. -- ___________________________________ Phoebe Suk-tak Chan, Ph.D. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Bldg. 149, 13th St., mailcode 149-2301 Charlestown, MA 02129 pho...@nmr.mgh.harvard.edu
Tue Jun 14 21:05:37 EDT 2011 /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons /usr/local/freesurfer/stable5_1_0/bin/trac-all -prep -c ./scripts/dmrirc_single_subject Subject 040826_cst SUBJECTS_DIR /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_inflated3 FREESURFER_HOME /usr/local/freesurfer/stable5_1_0 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos4.0_x86_64/stable5_1_0 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110514 phoebe deqi Linux deqi 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 407552 total used free shared buffers cached Mem: 49444976 28266052 21178924 0 1082748 20974188 -/+ buffers/cache: 6209116 43235860 Swap: 16787904 252 16787652 ######################################## Program versions: $Id: trac-all,v 1.22.2.6 2011/05/24 06:49:09 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/06/15-01:05:37-GMT BuildTimeStamp: May 14 2011 05:56:56 CVS: $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ User: phoebe Machine: deqi Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ $Id: mri_cvs_register,v 1.15.2.5 2011/05/13 23:40:25 lzollei Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/06/15-01:05:38-GMT BuildTimeStamp: May 24 2011 05:40:10 CVS: User: phoebe Machine: deqi Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/06/15-01:05:38-GMT BuildTimeStamp: May 24 2011 05:40:10 CVS: User: phoebe Machine: deqi Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/06/15-01:05:38-GMT BuildTimeStamp: May 24 2011 05:40:10 CVS: User: phoebe Machine: deqi Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/06/15-01:05:38-GMT BuildTimeStamp: May 24 2011 05:40:10 CVS: User: phoebe Machine: deqi Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 New invocation of trac-preproc phoebe deqi Linux deqi 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 407552 total used free shared buffers cached Mem: 49444976 28267092 21177884 0 1082748 20974188 -/+ buffers/cache: 6210156 43234820 Swap: 16787904 252 16787652 #------------------------------------- /usr/local/freesurfer/stable5_1_0/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Jun 14 21:05:38 EDT 2011 mri_convert /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/dcm/040826_cst/040826_cst_009_00001.dcm /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_orig.nii.gz mri_convert /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/dcm/040826_cst/040826_cst_009_00001.dcm /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/dcm/040826_cst/040826_cst_009_00001.dcm... Getting Series No INFO: Found 1502 files in /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/dcm/040826_cst INFO: Scanning for Series Number 9 Scanning Directory INFO: found 1499 files in series INFO: loading series header info. RunNo = 8 WARNING: Run 8 appears to be truncated Slice = 58, nthframe = 24, nframes = 25, 0 INFO: sorting. INFO: (256 256 58), nframes = 25, ismosaic=0 PE Dir COL COL ERROR: nlist (1499) > nslices (58) x frames (25) ERROR: dump file list into fileinfo.txt. ERROR: check for consistency ERROR: set nlist = nslices*nframes. FileName /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/dcm/040826_cst/040826_cst_009_00001.dcm Identification NumarisVer syngo MR 2002B 4VA21A ScannerModel Sonata PatientName CHAN^SUK TAK Date and time StudyDate 20040826 StudyTime 155340.937000 SeriesTime 163347.250000 AcqTime 162918.782481 Acquisition parameters PulseSeq ep_b0 Protocol ep2d_diff_MDDW_12di PhEncDir COL EchoNo 0 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9500 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 8 SeriesNo 9 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 25 SliceArraylSize 60 IsMosaic 0 ImgPos 131.7500 150.4502 -40.3564 VolRes 1.0000 1.0000 2.2000 VolDim 256 256 58 Vc -0.9999 -0.0016 0.0156 Vr 0.0000 -0.9945 -0.1045 Vs 0.0157 -0.1045 0.9944 VolCenter 4.7679 16.2731 11.7061 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=9500.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-0.999877, -0.0016419, 0.0156213) j_ras = (3.34102e-08, -0.994522, -0.104528) k_ras = (0.0157073, -0.104516, 0.994399) writing to /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_orig.nii.gz... mri_probedicom --i /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/dcm/040826_cst/040826_cst_009_00001.dcm > /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dcminfo.dat cp /autofs/space/guasha_001/users/phoebe/strab_func_chan4/siemens_12_qeh_bvec_strab /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_orig.mghdti.bvecs cp /autofs/space/guasha_001/users/phoebe/strab_func_chan4/siemens_12_qeh_bval_strab /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_orig.mghdti.bvals flip4fsl /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_orig.nii.gz /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2.2 fslswapdim /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_orig.nii.gz x -y z /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_orig_flip.nii.gz INFO: found /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_orig_flip.mghdti.bvecs /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/bvecs mv -f /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_orig_flip.mghdti.bvals /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/bvals eddy_correct /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_orig_flip.nii.gz /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi.nii.gz 0 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0000 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0001 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0002 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0003 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0004 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0005 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0006 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0007 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0008 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0009 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0010 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0011 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0012 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0013 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0014 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0015 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0016 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0017 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0018 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0019 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0020 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0021 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0022 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0023 processing /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_tmp0024 mv -f /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/bvecs /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/bvecs.norot xfmrot /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi.ecclog /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/bvecs.norot /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/bvecs fslroi /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi.nii.gz /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz 0 Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> fslroi <input> <output> <tmin> <tsize> fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize> Note: indexing (in both time and space) starts with 0 not 1! Linux deqi 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Tue Jun 14 21:27:55 EDT 2011
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