hello i am trying to process the dti data with trac-all. I am new to tracula my input images are 3300 dicoms, 60 slices and 55 dti diffusions i have attached my dmrirc_single_subject file
i did the following command:
trac-all -prep -c /Studies/MJMRI/DTI/dmrirc_single_subject
and got the result:
INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012
INFO: Diffusion root is /Studies/MJMRI/MJ0012
Actual FREESURFER_HOME /Applications/freesurfer
trac-preproc -c /Studies/MJMRI/MJ0012/freesurfer/scripts/dmrirc.local -log
/Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.log -cmd
/Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.cmd
#-------------------------------------
/Applications/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Mon Feb 11 12:41:04 CST 2013
mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1
/Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz
mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1
/Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1...
Starting DICOMRead2()
dcmfile = /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1
dcmdir = /Studies/MJMRI/MJ0012//s780
Ref Series No = 13
Found 3304 files, checking for dicoms
Found 3300 dicom files in series.
First Sorting
Computing Slice Direction
Vs: 0 0 2
Vs: 0 0 1
Second Sorting
Counting frames
nframes = 55
nslices = 60
ndcmfiles = 3300
PE Dir = COL (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2.1--
jpegUID: --1.2.840.10008.1.2.4--
Loading pixel data
TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (-0, -0, 1)
writing to /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz...
mri_probedicom --i /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 >
/Studies/MJMRI/MJ0012/freesurfer/dmri/dcminfo.dat
flip4fsl /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz
/Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 2
fslswapdim /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz x -y z
/Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological
/Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz
INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvals,
converting to FSL format
INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvecs,
converting to FSL format
mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs
/Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs
mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvals
/Studies/MJMRI/MJ0012/freesurfer/dmri/bvals
eddy_correct /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz
/Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz 0
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0000
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0001
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0002
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0003
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0004
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0005
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0006
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0007
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0008
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0009
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0010
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0011
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0012
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0013
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0014
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0015
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0016
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0017
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0018
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0019
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0020
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0021
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0022
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0023
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0024
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0025
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0026
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0027
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0028
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0029
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0030
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0031
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0032
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0033
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0034
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0035
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0036
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0037
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0038
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0039
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0040
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0041
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0042
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0043
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0044
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0045
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0046
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0047
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0048
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0049
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0050
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0051
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0052
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0053
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0054
mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs
/Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot
xfmrot /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.ecclog
/Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot
/Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs
fslroi /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz
/Studies/MJMRI/MJ0012/freesurfer/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!
Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun
7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Mon Feb 11 13:25:16 CST 2013
can you tell me how to fix this?
Thanks
Jon Wieser
UW-Milwaukee
dmrirc_single_subject
Description: Binary data
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