Hi Liliana - It looks like you are using a very old FreeSurfer build (from
2016) and an old TRACULA configuration file. You should update to the latest
version of FreeSurfer and follow the instructions on the wiki for how to set up
TRACULA. We have many more tracts now and the naming has changed. To
reconstruct the subset of tracts you want with the new version, you just need
this in the config file:
set pathlist = (lh.cst rh.cst lh.uf rh.uf lh.cbd rh.cbd lh.cbv rh.cbv)
Anastasia.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Liliana Wu
<liliana...@mail.utoronto.ca>
Sent: Friday, August 19, 2022 1:43 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA - preprocessing error
External Email - Use Caution
Here is the error log information:
INFO: SUBJECTS_DIR is /home/lwu/Desktop/OIRM02/trc
INFO: Diffusion root is /home/lwu/Desktop/OIRM02/trc/output
Actual FREESURFER_HOME /usr/local/freesurfer
trac-preproc -c /home/lwu/Desktop/OIRM02/trc/output/OIRM02/scripts/dmrirc.local
-log /home/lwu/Desktop/OIRM02/trc/output/OIRM02/scripts/trac-all.log -cmd
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/scripts/trac-all.cmd
#-------------------------------------
/usr/local/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Fri Aug 19 13:27:09 EDT 2022
mri_convert --bvec-voxel /home/lwu/Desktop/OIRM02/trc/OIRM02/OIRM02_DTI.nii.gz
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel
/home/lwu/Desktop/OIRM02/trc/OIRM02/OIRM02_DTI.nii.gz
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/lwu/Desktop/OIRM02/trc/OIRM02/OIRM02_DTI.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999551, 0.00440173, 0.0296355)
j_ras = (-0.0024424, 0.973885, -0.227028)
k_ras = (0.0298609, 0.226998, 0.973437)
writing to /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz...
cp /home/lwu/Desktop/OIRM02/trc/OIRM02/bvecs_path.txt
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvecs
cp /home/lwu/Desktop/OIRM02/trc/OIRM02/bvals_path.txt
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvals
mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvecs.tmp
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvecs
mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvals.tmp
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvals
orientLAS /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -8
mri_convert -oni 122 -onj 122 -onk 70 -oid -0.999551 0.00440173 0.0296355 -ojd
-0.0024424 0.973885 -0.227028 -okd 0.0298609 0.226998 0.973437 -oc -0.949776
14.1753 25.1557 -rt nearest
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 122 -onj 122 -onk 70 -oid -0.999551 0.00440173 0.0296355
-ojd -0.0024424 0.973885 -0.227028 -okd 0.0298609 0.226998 0.973437 -oc
-0.949776 14.1753 25.1557 -rt nearest
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz
normalizing out_i_direction: (-0.999551, 0.00440173, 0.0296355) -> (-0.999551,
0.00440173, 0.0296355)
normalizing out_j_direction: (-0.0024424, 0.973885, -0.227028) -> (-0.0024424,
0.973885, -0.227028)
normalizing out_k_direction: (0.0298609, 0.226998, 0.973437) -> (0.0298609,
0.226998, 0.973437)
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999551, 0.00440173, 0.0296355)
j_ras = (-0.0024424, 0.973885, -0.227028)
k_ras = (0.0298609, 0.226998, 0.973437)
Reslicing using nearest
writing to
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz...
INFO: found /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvals,
copying
INFO: found /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvecs,
converting to LAS
mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.bvecs
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvecs
mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.bvals
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvals
eddy_correct
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.nii.gz 0
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0000
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0001
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0002
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0003
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0004
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0005
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0006
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0007
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0008
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0009
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0010
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0011
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0012
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0013
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0014
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0015
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0016
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0017
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0018
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0019
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0020
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0021
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0022
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0023
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0024
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0025
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0026
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0027
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0028
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0029
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0030
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0031
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0032
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0033
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0034
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0035
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0036
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0037
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0038
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0039
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0040
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0041
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0042
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0043
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0044
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0045
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0046
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0047
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0048
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0049
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0050
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0051
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0052
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0053
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0054
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0055
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0056
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0057
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0058
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0059
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0060
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0061
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0062
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0063
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0064
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0065
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0066
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0067
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0068
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0069
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0070
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0071
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0072
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0073
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0074
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0075
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0076
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0077
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0078
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0079
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0080
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0081
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0082
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0083
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0084
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0085
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0086
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0087
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0088
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0089
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0090
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0091
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0092
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0093
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0094
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0095
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0096
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0097
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0098
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0099
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0100
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0101
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0102
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0103
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0104
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0105
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0106
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0107
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0108
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0109
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0110
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0111
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0112
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0113
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0114
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0115
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0116
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0117
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0118
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0119
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0120
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0121
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0122
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0123
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0124
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0125
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0126
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0127
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0128
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0129
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0130
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0131
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0132
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0133
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0134
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0135
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0136
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0137
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0138
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0139
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0140
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0141
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0142
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0143
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0144
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0145
mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvecs
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvecs.norot
xfmrot /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.ecclog
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvecs.norot
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvecs
ln -sf /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.nii.gz
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/data.nii.gz
mri_convert --frame 6 13 20 27 34 45 56 67 79 90 100 111 122 133 145
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.nii.gz
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb.nii.gz
mri_convert.bin --frame 6 13 20 27 34 45 56 67 79 90 100 111 122 133 145
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.nii.gz
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999551, 0.00440173, 0.0296355)
j_ras = (-0.0024424, 0.973885, -0.227028)
k_ras = (0.0298609, 0.226998, 0.973437)
keeping frames 6 13 20 27 34 45 56 67 79 90 100 111 122 133 145
writing to /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb.nii.gz...
mri_concat --i /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb.nii.gz
--mean --o /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb.nii.gz
ninputs = 1
Checking inputs
nframestot = 15
Allocing output
Done allocing
nframes = 15
Computing mean across frames
Writing to /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb.nii.gz
bet /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb.nii.gz
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb_brain.nii.gz -m -f 0.3
mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb_brain_mask.nii.gz
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/diff
#-------------------------------------
#@# Image quality assessment Fri Aug 19 13:42:27 EDT 2022
/usr/local/freesurfer/bin/dmri_motion --dwi
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz --mat
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.ecclog --bval
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvals --T 227.122620 --out
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_motion.txt
cwd /home/lwu/Desktop/OIRM02/trc
cmdline /usr/local/freesurfer/bin/dmri_motion --dwi
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz --mat
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.ecclog --bval
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvals --T 227.122620 --out
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_motion.txt
sysname Linux
hostname il-isotropic
machine x86_64
user lwu
Output motion measure file:
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_motion.txt
Input transform file: /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.ecclog
Input DWI file: /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz
Input b-value table: /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvals
Low-b image intensity threshold: 227.123
Nominal diffusivity: 0.001
Loading volume-to-baseline affine transformations
Computing between-volume head motion measures
INFO: Processed transforms for 146 volumes
Loading DWI volume series from
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz
Loading b-value table from /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvals
Computing within-volume head motion measures
Done in 6.688 sec.
dmri_motion done
#-------------------------------------
#@# Inter-subject registration Fri Aug 19 13:42:34 EDT 2022
flirt -in /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb_brain.nii.gz
-ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb_brain_mni.nii.gz -omat
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/xfms/diff2mni.mat -cost corratio
convert_xfm -omat
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/xfms/mni2diff.mat -inverse
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/xfms/diff2mni.mat
#-------------------------------------
#@# Masks Fri Aug 19 13:42:43 EDT 2022
WARN: Could not find /home/lwu/Desktop/OIRM02/trc/OIRM02/mri/aparc+aseg.mgz
WARN: You will not be able to complete TRACULA processing without it
ln -sf
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/diff/lowb_brain_mask.nii.gz
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/nodif_brain_mask.nii.gz
#-------------------------------------
#@# Tensor fit Fri Aug 19 13:42:43 EDT 2022
dtifit -k /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.nii.gz -m
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/diff/lowb_brain_mask.nii.gz
-r /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvecs -b
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvals -o
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dtifit
0 122 0 122 0 70
0 slices processed
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#-------------------------------------
#@# Priors Fri Aug 19 13:42:49 EDT 2022
/usr/local/freesurfer/bin/dmri_train --outdir
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/mni --out
lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr
rh.unc_AS_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr
lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr --slist
/tmp/subj33.OIRM02.18847.txt --trk dlabel/mni/lh.cst_AS.bbr.trk
dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk
dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk
dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk
dlabel/mni/rh.ccg_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask
dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 --rois
dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz
dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz
dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz
dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz
dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz
dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz
dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz
--bmask
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/mni/lowb_brain_mask.bbr.nii.gz
--fa /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dtifit_FA.nii.gz --cptdir
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/diff --reg
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/xfms/mni2diff.bbr.mat --ncpts 6
6 5 5 5 5 4 4 --trunc
ERROR: fio_pushd: /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/mni
cwd /home/lwu/Desktop/OIRM02/trc
cmdline /usr/local/freesurfer/bin/dmri_train --outdir
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/mni --out
lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr
rh.unc_AS_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr
lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr --slist
/tmp/subj33.OIRM02.18847.txt --trk dlabel/mni/lh.cst_AS.bbr.trk
dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk
dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk
dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk
dlabel/mni/rh.ccg_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask
dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 --rois
dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz
dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz
dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz
dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz
dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz
dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz
dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz
--bmask
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/mni/lowb_brain_mask.bbr.nii.gz
--fa /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dtifit_FA.nii.gz --cptdir
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/diff --reg
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/xfms/mni2diff.bbr.mat --ncpts 6
6 5 5 5 5 4 4 --trunc
sysname Linux
hostname il-isotropic
machine x86_64
user lwu
Output directory: /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/mni
Output directory in test subject's space:
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/diff
Output base: lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr
lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr
rh.cab_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr
Training subject directory list: /tmp/subj33.OIRM02.18847.txt
Location of streamline files relative to base: dlabel/mni/lh.cst_AS.bbr.trk
dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk
dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk
dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk
dlabel/mni/rh.ccg_PP.bbr.trk
Location of start ROI files relative to base:
dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz
dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz
dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz
dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz
Location of end ROI files relative to base:
dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz
dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz
dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz
dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz
Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz
Label ID's from aparc+aseg to add to cortex mask: 16 16 0 0 0 0 0 0
Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz
Brain mask for output subject: Segmentation fault (core dumped)
Linux il-isotropic 5.4.0-122-generic #138~18.04.1-Ubuntu SMP Fri Jun 24
14:14:03 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Fri Aug 19 13:42:49 EDT 2022
________________________________
From: Liliana Wu <liliana...@mail.utoronto.ca>
Sent: August 19, 2022 12:44 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: TRACULA - preprocessing error
Hi,
I ran the preprocessing command trac-all -prep -c $SUBJECTS_DIR/script and I am
getting the following error
ERROR: fio_pushd: /home/lwu/Desktop/OIRM02/trc/OIRM02/dlabel/mni
I don’t see the mni folder created in my files… I am trying to only reconstruct
the following pathways.
set pathlist = ( lh.cst_JL rh.cst_JL \
lh.unc_JL rh.unc_JL \
lh.ccg_PP rh.ccg_PP \
lh.cab_PP rh.cab_PP)
set ncpts = (6 6 5 5 5 5 4 4)
I appreciate any help,
Thank you
Liliana
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