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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