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