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
[email protected]
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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