Dear fellow researchers,

I am running tracula pre-processing step, and the computer showed an error
message:
Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz
Brain mask for output subject: Segmentation fault (core dumped)
Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC
2016 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Sun Aug  6 23:37:59 EDT 2017

I am sure that I have the aparc+aseg file in the right directory but it
showed that the files are missing.....

I would be really appreciated if anyone could please help!!! Thanks so
much!!!

PS: I attached trac-all.log as an attachment. Thanks

Sincerely,

Ariel
Sun Aug  6 18:19:37 EDT 2017
/media/brain/brains/TN_retro/Tracula
/usr/local/freesurfer/bin/trac-all
-prep -c dmrirc
Subject AN01
SUBJECTS_DIR /media/brain/brains/TN_retro/Tracula
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
root
Brain
Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc      15430 
maxlocks     unlimited
maxsignal    15430 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

             total       used       free     shared    buffers     cached
Mem:       3971612    3064872     906740      53912     679792    1089976
-/+ buffers/cache:    1295104    2676508
Swap:      4117500      15804    4101696

########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/08/06-22:19:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/08/06-22:19:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/08/06-22:19:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/08/06-22:19:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/08/06-22:19:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/08/06-22:19:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/08/06-22:19:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 


New invocation of trac-preproc


root
Brain
Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc      15430 
maxlocks     unlimited
maxsignal    15430 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

             total       used       free     shared    buffers     cached
Mem:       3971612    3068316     903296      53912     679856    1092544
-/+ buffers/cache:    1295916    2675696
Swap:      4117500      15804    4101696

#-------------------------------------
/usr/local/freesurfer/bin/trac-preproc 
#-------------------------------------
#@# Image corrections Sun Aug  6 18:19:37 EDT 2017
mri_convert --bvec-voxel /media/brain/brains/TN_retro/Tracula/dicom/IM000000.dcm /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /media/brain/brains/TN_retro/Tracula/dicom/IM000000.dcm /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /media/brain/brains/TN_retro/Tracula/dicom/IM000000.dcm...
Starting DICOMRead2()
dcmfile = /media/brain/brains/TN_retro/Tracula/dicom/IM000000.dcm
dcmdir = /media/brain/brains/TN_retro/Tracula/dicom
Ref Series No = 5
Found 2730 files, checking for dicoms
Found 2728 dicom files in series.
First Sorting
Computing Slice Direction
Vs: 0 0 3
Vs: 0 0 1
Second Sorting
IsDWI = 1, IsPhilipsDWI = 0
Counting frames
nframes = 62
nslices = 44
ndcmfiles = 2728
PE Dir = COL (dicom read)
Loading pixel data
TR=12000.00, TE=86.60, TI=0.00, flip angle=90.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (-0, -0, 1)
writing to /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz...
Saving bvals and bvecs
mv -f /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.voxel_space.bvecs /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.bvecs
mri_probedicom --i /media/brain/brains/TN_retro/Tracula/dicom/IM000000.dcm > /media/brain/brains/TN_retro/Tracula/AN01/dmri/dcminfo.dat
cp /media/brain/brains/TN_retro/Tracula/bvecs.bvec /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.bvecs
cp /media/brain/brains/TN_retro/Tracula/bvals.bval /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.bvals
mv -f /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvecs.tmp /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.bvecs
mv -f /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvals.tmp /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.bvals
orientLAS /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 2.63672
mri_convert -oni 256 -onj 256 -onk 44 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc 0.116997 22.4685 9.0268 -rt nearest /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 44 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc 0.116997 22.4685 9.0268 -rt nearest /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig_las.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz...
TR=12000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (-0, -0, 1)
Reslicing using nearest 
writing to /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig_las.nii.gz...
INFO: found /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.bvals, copying
INFO: found /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.bvecs, converting to LAS
mv -f /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig_las.bvecs /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvecs
mv -f /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig_las.bvals /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvals
eddy_correct /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig_las.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.nii.gz 0
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0000
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0001
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0002
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0003
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0004
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0005
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0006
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0007
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0008
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0009
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0010
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0011
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0012
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0013
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0014
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0015
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0016
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0017
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0018
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0019
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0020
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0021
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0022
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0023
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0024
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0025
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0026
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0027
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0028
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0029
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0030
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0031
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0032
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0033
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0034
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0035
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0036
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0037
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0038
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0039
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0040
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0041
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0042
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0043
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0044
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0045
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0046
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0047
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0048
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0049
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0050
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0051
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0052
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0053
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0054
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0055
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0056
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0057
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0058
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0059
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0060
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0061
mv -f /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvecs /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvecs.norot
xfmrot /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.ecclog /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvecs.norot /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvecs
ln -sf /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dmri/data.nii.gz
mri_convert --frame 0 1 /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb.nii.gz
mri_convert.bin --frame 0 1 /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
keeping frames 0 1
writing to /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb.nii.gz...
mri_concat --i /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb.nii.gz --mean --o /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb.nii.gz
ninputs = 1
Checking inputs
nframestot = 2
Allocing output
Done allocing
nframes = 2
Computing mean across frames
Writing to /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb.nii.gz
bet /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb_brain.nii.gz -m -f 0.3
mv -f /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb_brain_mask.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dlabel/diff
#-------------------------------------
#@# Image quality assessment Sun Aug  6 18:55:29 EDT 2017
/usr/local/freesurfer/bin/dmri_motion --dwi /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz --mat /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.ecclog --bval /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvals --T 945.000000 --out /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_motion.txt


cwd /media/brain/brains/TN_retro/Tracula
cmdline /usr/local/freesurfer/bin/dmri_motion --dwi /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz --mat /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.ecclog --bval /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvals --T 945.000000 --out /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_motion.txt 
sysname  Linux
hostname Brain
machine  x86_64
user     root
Output motion measure file: /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_motion.txt
Input transform file: /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.ecclog
Input DWI file: /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz
Input b-value table: /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvals
Low-b image intensity threshold: 945
Nominal diffusivity: 0.001
Loading volume-to-baseline affine transformations
Computing between-volume head motion measures
INFO: Processed transforms for 62 volumes
Loading DWI volume series from /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz
Loading b-value table from /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvals
Computing within-volume head motion measures
Done in 9.804 sec.
dmri_motion done
#-------------------------------------
#@# Inter-subject registration Sun Aug  6 18:55:39 EDT 2017
flirt -in /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb_brain.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb_brain_mni.nii.gz -omat /media/brain/brains/TN_retro/Tracula/AN01/dmri/xfms/diff2mni.mat -cost corratio
convert_xfm -omat /media/brain/brains/TN_retro/Tracula/AN01/dmri/xfms/mni2diff.mat -inverse /media/brain/brains/TN_retro/Tracula/AN01/dmri/xfms/diff2mni.mat
#-------------------------------------
#@# Masks Sun Aug  6 18:56:21 EDT 2017
ln -sf /media/brain/brains/TN_retro/Tracula/AN01/dlabel/diff/lowb_brain_mask.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dmri/nodif_brain_mask.nii.gz
#-------------------------------------
#@# Tensor fit Sun Aug  6 18:56:21 EDT 2017
dtifit -k /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.nii.gz -m /media/brain/brains/TN_retro/Tracula/AN01/dlabel/diff/lowb_brain_mask.nii.gz -r /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvecs -b /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvals -o /media/brain/brains/TN_retro/Tracula/AN01/dmri/dtifit
0 256 0 256 0 44
0 slices processed
1 slices processed
2 slices processed
3 slices processed
4 slices processed
5 slices processed
6 slices processed
7 slices processed
8 slices processed
9 slices processed
10 slices processed
11 slices processed
12 slices processed
13 slices processed
14 slices processed
15 slices processed
16 slices processed
17 slices processed
18 slices processed
19 slices processed
20 slices processed
21 slices processed
22 slices processed
23 slices processed
24 slices processed
25 slices processed
26 slices processed
27 slices processed
28 slices processed
29 slices processed
30 slices processed
31 slices processed
32 slices processed
33 slices processed
34 slices processed
35 slices processed
36 slices processed
37 slices processed
38 slices processed
39 slices processed
40 slices processed
41 slices processed
42 slices processed
43 slices processed
#-------------------------------------
#@# Priors Sun Aug  6 18:56:40 EDT 2017
/usr/local/freesurfer/bin/dmri_train --outdir /media/brain/brains/TN_retro/Tracula/AN01/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.AN01.17092.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_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 10 49 0 0 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.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_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/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_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 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.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /media/brain/brains/TN_retro/Tracula/AN01/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /media/brain/brains/TN_retro/Tracula/AN01/dmri/dtifit_FA.nii.gz --cptdir /media/brain/brains/TN_retro/Tracula/AN01/dlabel/diff --reg /media/brain/brains/TN_retro/Tracula/AN01/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc
ERROR: fio_pushd: /media/brain/brains/TN_retro/Tracula/AN01/dlabel/mni


cwd /media/brain/brains/TN_retro/Tracula
cmdline /usr/local/freesurfer/bin/dmri_train --outdir /media/brain/brains/TN_retro/Tracula/AN01/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.AN01.17092.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_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 10 49 0 0 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.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_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/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_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 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.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /media/brain/brains/TN_retro/Tracula/AN01/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /media/brain/brains/TN_retro/Tracula/AN01/dmri/dtifit_FA.nii.gz --cptdir /media/brain/brains/TN_retro/Tracula/AN01/dlabel/diff --reg /media/brain/brains/TN_retro/Tracula/AN01/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc 
sysname  Linux
hostname Brain
machine  x86_64
user     root
Output directory: /media/brain/brains/TN_retro/Tracula/AN01/dlabel/mni
Output directory in test subject's space: /media/brain/brains/TN_retro/Tracula/AN01/dlabel/diff
Output base: lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr
Training subject directory list: /tmp/subj33.AN01.17092.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.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_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.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_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/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_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.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_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.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_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/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_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.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_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 10 49 0 0 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: Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Sun Aug  6 18:56:40 EDT 2017



New invocation of trac-all


Sun Aug  6 23:00:54 EDT 2017
/media/brain/brains/TN_retro/Tracula
/usr/local/freesurfer/bin/trac-all
-prep -c dmrirc
Subject AN01
SUBJECTS_DIR /media/brain/brains/TN_retro/Tracula
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
root
Brain
Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc      15430 
maxlocks     unlimited
maxsignal    15430 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

             total       used       free     shared    buffers     cached
Mem:       3971612    3026568     945044      56200     666840    1225024
-/+ buffers/cache:    1134704    2836908
Swap:      4117500      22828    4094672

########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/08/07-03:00:55-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/08/07-03:00:55-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/08/07-03:00:55-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/08/07-03:00:55-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/08/07-03:00:55-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/08/07-03:00:55-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/08/07-03:00:55-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: root  Machine: Brain  Platform: Linux  PlatformVersion: 4.2.0-27-generic  CompilerName: GCC  CompilerVersion: 40400 


New invocation of trac-preproc


root
Brain
Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc      15430 
maxlocks     unlimited
maxsignal    15430 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

             total       used       free     shared    buffers     cached
Mem:       3971612    3028412     943200      56200     666904    1224960
-/+ buffers/cache:    1136548    2835064
Swap:      4117500      22828    4094672

#-------------------------------------
/usr/local/freesurfer/bin/trac-preproc 
#-------------------------------------
#@# Image corrections Sun Aug  6 23:00:55 EDT 2017
mri_convert --bvec-voxel /media/brain/brains/TN_retro/Tracula/dicom/IM000000.dcm /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /media/brain/brains/TN_retro/Tracula/dicom/IM000000.dcm /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /media/brain/brains/TN_retro/Tracula/dicom/IM000000.dcm...
Starting DICOMRead2()
dcmfile = /media/brain/brains/TN_retro/Tracula/dicom/IM000000.dcm
dcmdir = /media/brain/brains/TN_retro/Tracula/dicom
Ref Series No = 5
Found 2730 files, checking for dicoms
Found 2728 dicom files in series.
First Sorting
Computing Slice Direction
Vs: 0 0 3
Vs: 0 0 1
Second Sorting
IsDWI = 1, IsPhilipsDWI = 0
Counting frames
nframes = 62
nslices = 44
ndcmfiles = 2728
PE Dir = COL (dicom read)
Loading pixel data
TR=12000.00, TE=86.60, TI=0.00, flip angle=90.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (-0, -0, 1)
writing to /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz...
Saving bvals and bvecs
mv -f /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.voxel_space.bvecs /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.bvecs
mri_probedicom --i /media/brain/brains/TN_retro/Tracula/dicom/IM000000.dcm > /media/brain/brains/TN_retro/Tracula/AN01/dmri/dcminfo.dat
cp /media/brain/brains/TN_retro/Tracula/bvecs.bvec /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.bvecs
cp /media/brain/brains/TN_retro/Tracula/bvals.bval /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.bvals
mv -f /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvecs.tmp /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.bvecs
mv -f /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvals.tmp /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.bvals
orientLAS /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 2.63672
mri_convert -oni 256 -onj 256 -onk 44 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc 0.116997 22.4685 9.0268 -rt nearest /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 44 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc 0.116997 22.4685 9.0268 -rt nearest /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig_las.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz...
TR=12000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (-0, -0, 1)
Reslicing using nearest 
writing to /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig_las.nii.gz...
INFO: found /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.bvals, copying
INFO: found /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.bvecs, converting to LAS
mv -f /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig_las.bvecs /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvecs
mv -f /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig_las.bvals /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvals
eddy_correct /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig_las.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.nii.gz 0
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0000
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0001
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0002
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0003
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0004
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0005
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0006
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0007
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0008
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0009
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0010
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0011
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0012
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0013
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0014
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0015
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0016
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0017
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0018
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0019
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0020
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0021
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0022
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0023
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0024
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0025
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0026
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0027
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0028
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0029
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0030
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0031
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0032
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0033
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0034
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0035
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0036
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0037
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0038
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0039
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0040
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0041
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0042
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0043
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0044
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0045
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0046
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0047
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0048
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0049
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0050
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0051
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0052
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0053
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0054
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0055
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0056
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0057
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0058
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0059
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0060
processing /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_tmp0061
mv -f /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvecs /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvecs.norot
xfmrot /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.ecclog /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvecs.norot /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvecs
ln -sf /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dmri/data.nii.gz
mri_convert --frame 0 1 /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb.nii.gz
mri_convert.bin --frame 0 1 /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
keeping frames 0 1
writing to /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb.nii.gz...
mri_concat --i /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb.nii.gz --mean --o /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb.nii.gz
ninputs = 1
Checking inputs
nframestot = 2
Allocing output
Done allocing
nframes = 2
Computing mean across frames
Writing to /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb.nii.gz
bet /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb_brain.nii.gz -m -f 0.3
mv -f /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb_brain_mask.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dlabel/diff
#-------------------------------------
#@# Image quality assessment Sun Aug  6 23:36:48 EDT 2017
/usr/local/freesurfer/bin/dmri_motion --dwi /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz --mat /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.ecclog --bval /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvals --T 945.000000 --out /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_motion.txt


cwd /media/brain/brains/TN_retro/Tracula
cmdline /usr/local/freesurfer/bin/dmri_motion --dwi /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz --mat /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.ecclog --bval /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvals --T 945.000000 --out /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_motion.txt 
sysname  Linux
hostname Brain
machine  x86_64
user     root
Output motion measure file: /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_motion.txt
Input transform file: /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.ecclog
Input DWI file: /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz
Input b-value table: /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvals
Low-b image intensity threshold: 945
Nominal diffusivity: 0.001
Loading volume-to-baseline affine transformations
Computing between-volume head motion measures
INFO: Processed transforms for 62 volumes
Loading DWI volume series from /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi_orig.nii.gz
Loading b-value table from /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvals
Computing within-volume head motion measures
Done in 9.858 sec.
dmri_motion done
#-------------------------------------
#@# Inter-subject registration Sun Aug  6 23:36:58 EDT 2017
flirt -in /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb_brain.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/brain/brains/TN_retro/Tracula/AN01/dmri/lowb_brain_mni.nii.gz -omat /media/brain/brains/TN_retro/Tracula/AN01/dmri/xfms/diff2mni.mat -cost corratio
convert_xfm -omat /media/brain/brains/TN_retro/Tracula/AN01/dmri/xfms/mni2diff.mat -inverse /media/brain/brains/TN_retro/Tracula/AN01/dmri/xfms/diff2mni.mat
#-------------------------------------
#@# Masks Sun Aug  6 23:37:40 EDT 2017
ln -sf /media/brain/brains/TN_retro/Tracula/AN01/dlabel/diff/lowb_brain_mask.nii.gz /media/brain/brains/TN_retro/Tracula/AN01/dmri/nodif_brain_mask.nii.gz
#-------------------------------------
#@# Tensor fit Sun Aug  6 23:37:40 EDT 2017
dtifit -k /media/brain/brains/TN_retro/Tracula/AN01/dmri/dwi.nii.gz -m /media/brain/brains/TN_retro/Tracula/AN01/dlabel/diff/lowb_brain_mask.nii.gz -r /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvecs -b /media/brain/brains/TN_retro/Tracula/AN01/dmri/bvals -o /media/brain/brains/TN_retro/Tracula/AN01/dmri/dtifit
0 256 0 256 0 44
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#-------------------------------------
#@# Priors Sun Aug  6 23:37:59 EDT 2017
/usr/local/freesurfer/bin/dmri_train --outdir /media/brain/brains/TN_retro/Tracula/AN01/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.AN01.19188.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_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 10 49 0 0 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.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_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/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_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 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.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /media/brain/brains/TN_retro/Tracula/AN01/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /media/brain/brains/TN_retro/Tracula/AN01/dmri/dtifit_FA.nii.gz --cptdir /media/brain/brains/TN_retro/Tracula/AN01/dlabel/diff --reg /media/brain/brains/TN_retro/Tracula/AN01/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc
ERROR: fio_pushd: /media/brain/brains/TN_retro/Tracula/AN01/dlabel/mni


cwd /media/brain/brains/TN_retro/Tracula
cmdline /usr/local/freesurfer/bin/dmri_train --outdir /media/brain/brains/TN_retro/Tracula/AN01/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.AN01.19188.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_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 10 49 0 0 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.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_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/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_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 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.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /media/brain/brains/TN_retro/Tracula/AN01/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /media/brain/brains/TN_retro/Tracula/AN01/dmri/dtifit_FA.nii.gz --cptdir /media/brain/brains/TN_retro/Tracula/AN01/dlabel/diff --reg /media/brain/brains/TN_retro/Tracula/AN01/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc 
sysname  Linux
hostname Brain
machine  x86_64
user     root
Output directory: /media/brain/brains/TN_retro/Tracula/AN01/dlabel/mni
Output directory in test subject's space: /media/brain/brains/TN_retro/Tracula/AN01/dlabel/diff
Output base: lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr
Training subject directory list: /tmp/subj33.AN01.19188.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.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_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.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_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/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_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.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_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.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_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/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_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.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_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 10 49 0 0 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: Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Sun Aug  6 23:37:59 EDT 2017

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