Hello, Freesurfer experts:
I am new to Tracula, and I followed your tutorial with your tutorial data, and
for the preprocessing pipeline, I got some errors when doing the tensor
fitting, here is the command:
trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial
and I looked over the trac-all.log and found that the problem is from the
command dmri_train, here is the errro log information:
'
/aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/dmri_train
--outdir
/aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/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.elmo.2005.25745.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
/aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni/lowb_brain_mask.bbr.nii.gz
--fa
/aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dtifit_FA.nii.gz
--cptdir
/aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/diff
--reg
/aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/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:
/aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni
cwd
/aramis/dataARAMIS/users/junhao.wen/dataset/Freesurfer/tutorial_data_new/diffusion_tutorial
cmdline
/aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/dmri_train
--outdir
/aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/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.elmo.2005.25745.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
/aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni/lowb_brain_mask.bbr.nii.gz
--fa
/aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dtifit_FA.nii.gz
--cptdir
/aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/diff
--reg
/aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/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 DELLEED1
machine x86_64
user wen
Output directory:
/aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni
Output directory in test subject's space:
/aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/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.elmo.2005.25745.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: [1] 1065 segmentation fault (core dumped)
--outdir --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr
'
and in the output structure /dlabel, I dont have the mni sub-folder, so I guess
I have some problems when doning the tensor fitting.
And I know in this process, we will need the aparc+aseg.mgz, but the in the
tutorial data diffusion_recons , for the subject of elmo.2005, I dont find
aparc+aseg.mgz in mri folder, and I just found aparc+aseg2diff.mgz image in
Diff001, instead, you use this volume???
I am stuck at this step, any advice will be appreciated:)
Thank in advance
Hao
Good day
Sat Dec 17 16:14:00 CET 2016
/aramis/dataARAMIS/users/junhao.wen/dataset/Freesurfer/tutorial_data_new/diffusion_tutorial
/aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/trac-all
-prep -c /aramis/dataARAMIS/users/junhao.wen/dataset/Freesurfer/tutorial_data_new/diffusion_tutorial/dmrirc.tutorial
Subject elmo.2005
SUBJECTS_DIR /aramis/dataARAMIS/users/junhao.wen/dataset/Freesurfer/tutorial_data_new/diffusion_recons
FREESURFER_HOME /aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos
Actual FREESURFER_HOME /aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
wen
DELLEED1
Linux DELLEED1 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun 29 20:22:11 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 63924
maxlocks unlimited
maxsignal 63924
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buffers cached
Mem: 16386724 15926464 460260 124040 163748 11855276
-/+ buffers/cache: 3907440 12479284
Swap: 7999484 178092 7821392
########################################
Program versions:
$Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $
mri_convert --all-info
ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/17-15:14:00-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
FLIRT version 6.0
$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
$Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $
ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/17-15:14:00-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/17-15:14:00-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/17-15:14:00-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/17-15:14:00-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
New invocation of trac-preproc
wen
DELLEED1
Linux DELLEED1 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun 29 20:22:11 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 63924
maxlocks unlimited
maxsignal 63924
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buffers cached
Mem: 16386724 15929240 457484 124188 163748 11855444
-/+ buffers/cache: 3910048 12476676
Swap: 7999484 178092 7821392
#-------------------------------------
/aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/trac-preproc
#-------------------------------------
#@# Image corrections Sat Dec 17 16:14:01 CET 2016
mri_convert /aramis/dataARAMIS/users/junhao.wen/dataset/Freesurfer/tutorial_data_new/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_orig.nii.gz
mri_convert /aramis/dataARAMIS/users/junhao.wen/dataset/Freesurfer/tutorial_data_new/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /aramis/dataARAMIS/users/junhao.wen/dataset/Freesurfer/tutorial_data_new/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm...
Getting Series No
INFO: Found 72 files in /aramis/dataARAMIS/users/junhao.wen/dataset/Freesurfer/tutorial_data_new/diffusion_tutorial/elmo.2005/orig
INFO: Scanning for Series Number 11
Scanning Directory
INFO: found 70 files in series
INFO: loading series header info.
RunNo = 10
WARNING: Run 1 appears to be truncated
Files Found: 70, Files Expected (lRep+1): 120
FileName /aramis/dataARAMIS/users/junhao.wen/dataset/Freesurfer/tutorial_data_new/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
Identification
NumarisVer syngo MR 2004A 4VA25A
ScannerModel Trio
PatientName Trio_calib_002_run2
Date and time
StudyDate 20050905
StudyTime 100821.656000
SeriesTime 104226.748000
AcqTime 104209.522496
Acquisition parameters
PulseSeq ep_b0#0
Protocol DIFFUSION_HighRes
PhEncDir COL
EchoNo 0
FlipAngle 90
EchoTime 100
InversionTime -1
RepetitionTime 10100
PhEncFOV 256
ReadoutFOV 256
Image information
RunNo 10
SeriesNo 11
ImageNo 1
NImageRows 1024
NImageCols 1024
NFrames 70
SliceArraylSize 60
IsMosaic 1
ImgPos 1048.1801 1002.6923 -265.4914
VolRes 2.0000 2.0000 2.0000
VolDim 128 128 60
Vc -0.9997 0.0244 0.0005
Vr -0.0238 -0.9764 0.2147
Vs 0.0057 0.2147 0.9767
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID unknown
INFO: sorting.
INFO: (128 128 60), nframes = 70, ismosaic=1
Numaris Version: syngo MR 2004A 4VA25A Maj = 4, Min=2, MinMin = 5
Repetition Time = 10100, TR = 10100 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.000 0.024 -0.006 -0.495;
-0.024 0.976 -0.215 -40.555;
0.000 0.215 0.977 12.503;
0.000 0.000 0.000 1.000;
This looks like an MGH DTI volume
MGH DTI SeqPack Info
0 ep_b0#0 0.000000 0
1 ep_b0#1 0.000000 1
2 ep_b0#2 0.000000 2
3 ep_b0#3 0.000000 3
4 ep_b0#4 0.000000 4
5 ep_b0#5 0.000000 5
6 ep_b0#6 0.000000 6
7 ep_b0#7 0.000000 7
8 ep_b0#8 0.000000 8
9 ep_b0#9 0.000000 9
10 ep_b700#0 700.000000 0
11 ep_b700#1 700.000000 1
12 ep_b700#2 700.000000 2
13 ep_b700#3 700.000000 3
14 ep_b700#4 700.000000 4
15 ep_b700#5 700.000000 5
16 ep_b700#6 700.000000 6
17 ep_b700#7 700.000000 7
18 ep_b700#8 700.000000 8
19 ep_b700#9 700.000000 9
20 ep_b700#10 700.000000 10
21 ep_b700#11 700.000000 11
22 ep_b700#12 700.000000 12
23 ep_b700#13 700.000000 13
24 ep_b700#14 700.000000 14
25 ep_b700#15 700.000000 15
26 ep_b700#16 700.000000 16
27 ep_b700#17 700.000000 17
28 ep_b700#18 700.000000 18
29 ep_b700#19 700.000000 19
30 ep_b700#20 700.000000 20
31 ep_b700#21 700.000000 21
32 ep_b700#22 700.000000 22
33 ep_b700#23 700.000000 23
34 ep_b700#24 700.000000 24
35 ep_b700#25 700.000000 25
36 ep_b700#26 700.000000 26
37 ep_b700#27 700.000000 27
38 ep_b700#28 700.000000 28
39 ep_b700#29 700.000000 29
40 ep_b700#30 700.000000 30
41 ep_b700#31 700.000000 31
42 ep_b700#32 700.000000 32
43 ep_b700#33 700.000000 33
44 ep_b700#34 700.000000 34
45 ep_b700#35 700.000000 35
46 ep_b700#36 700.000000 36
47 ep_b700#37 700.000000 37
48 ep_b700#38 700.000000 38
49 ep_b700#39 700.000000 39
50 ep_b700#40 700.000000 40
51 ep_b700#41 700.000000 41
52 ep_b700#42 700.000000 42
53 ep_b700#43 700.000000 43
54 ep_b700#44 700.000000 44
55 ep_b700#45 700.000000 45
56 ep_b700#46 700.000000 46
57 ep_b700#47 700.000000 47
58 ep_b700#48 700.000000 48
59 ep_b700#49 700.000000 49
60 ep_b700#50 700.000000 50
61 ep_b700#51 700.000000 51
62 ep_b700#52 700.000000 52
63 ep_b700#53 700.000000 53
64 ep_b700#54 700.000000 54
65 ep_b700#55 700.000000 55
66 ep_b700#56 700.000000 56
67 ep_b700#57 700.000000 57
68 ep_b700#58 700.000000 58
69 ep_b700#59 700.000000 59
bValue = 700
nB0 = 10
nDir = 60
GradFile /aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/diffusion/mgh-dti-seqpack/gradient_mgh_dti60.gdt
FileName /aramis/dataARAMIS/users/junhao.wen/dataset/Freesurfer/tutorial_data_new/diffusion_tutorial/elmo.2005/orig/656000-11-4141.dcm
Identification
NumarisVer syngo MR 2004A 4VA25A
ScannerModel Trio
PatientName Trio_calib_002_run2
Date and time
StudyDate 20050905
StudyTime 100821.656000
SeriesTime 104226.748000
AcqTime 104350.522512
Acquisition parameters
PulseSeq ep_b700#59
Protocol DIFFUSION_HighRes
PhEncDir COL
EchoNo 0
FlipAngle 90
EchoTime 100
InversionTime -1
RepetitionTime 10100
PhEncFOV 256
ReadoutFOV 256
Image information
RunNo 10
SeriesNo 11
ImageNo 4141
NImageRows 1024
NImageCols 1024
NFrames 70
SliceArraylSize 60
IsMosaic 1
ImgPos 1048.1801 1002.6923 -265.4914
VolRes 2.0000 2.0000 2.0000
VolDim 128 128 60
Vc -0.9997 0.0244 0.0005
Vr -0.0238 -0.9764 0.2147
Vs 0.0057 0.2147 0.9767
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID unknown
UseSliceScaleFactor 0 (slice 0: 1)
sagrev = 1, correv =1, trarev = 0
Vs = 0.0057 0.214665 0.976671
INFO: no Siemens slice order reversal detected (good!).
TR=10100.00, TE=100.00, TI=-1.00, flip angle=90.00
i_ras = (-0.999702, 0.0244268, 0.000465598)
j_ras = (-0.023757, -0.976382, 0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
writing to /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_orig.nii.gz...
Saving bvals and bvecs
mri_probedicom --i /aramis/dataARAMIS/users/junhao.wen/dataset/Freesurfer/tutorial_data_new/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm > /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dcminfo.dat
flip4fsl /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_orig.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 8
fslswapdim /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_orig.nii.gz x -y z /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_orig_flip.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_orig_flip.nii.gz
INFO: found /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_orig.mghdti.bvals, converting to FSL format
INFO: found /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_orig.mghdti.bvecs, converting to FSL format
mv -f /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_orig_flip.mghdti.bvecs /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/bvecs
mv -f /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_orig_flip.mghdti.bvals /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/bvals
eddy_correct /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_orig_flip.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz 0
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0000
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0001
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0002
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0003
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0004
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0005
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0006
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0007
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0008
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0009
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0010
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0011
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0012
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0013
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0014
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0015
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0016
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0017
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0018
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0019
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0020
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0021
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0022
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0023
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0024
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0025
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0026
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0027
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0028
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0029
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0030
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0031
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0032
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0033
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0034
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0035
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0036
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0037
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0038
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0039
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0040
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0041
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0042
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0043
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0044
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0045
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0046
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0047
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0048
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0049
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0050
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0051
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0052
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0053
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0054
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0055
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0056
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0057
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0058
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0059
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0060
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0061
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0062
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0063
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0064
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0065
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0066
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0067
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0068
processing /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_tmp0069
mv -f /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/bvecs /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/bvecs.norot
xfmrot /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.ecclog /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/bvecs.norot /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/bvecs
ln -sf /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/data.nii.gz
mri_convert --frame 0 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame0.nii.gz
mri_convert --frame 0 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame0.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999701, 0.0244268, 0.000465598)
j_ras = (0.023757, 0.976382, -0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
keeping frame 0
writing to /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame0.nii.gz...
mri_convert --frame 1 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame1.nii.gz
mri_convert --frame 1 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame1.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999701, 0.0244268, 0.000465598)
j_ras = (0.023757, 0.976382, -0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
keeping frame 1
writing to /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame1.nii.gz...
mri_convert --frame 2 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame2.nii.gz
mri_convert --frame 2 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame2.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999701, 0.0244268, 0.000465598)
j_ras = (0.023757, 0.976382, -0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
keeping frame 2
writing to /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame2.nii.gz...
mri_convert --frame 3 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame3.nii.gz
mri_convert --frame 3 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame3.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999701, 0.0244268, 0.000465598)
j_ras = (0.023757, 0.976382, -0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
keeping frame 3
writing to /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame3.nii.gz...
mri_convert --frame 4 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame4.nii.gz
mri_convert --frame 4 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame4.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999701, 0.0244268, 0.000465598)
j_ras = (0.023757, 0.976382, -0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
keeping frame 4
writing to /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame4.nii.gz...
mri_convert --frame 5 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame5.nii.gz
mri_convert --frame 5 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame5.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999701, 0.0244268, 0.000465598)
j_ras = (0.023757, 0.976382, -0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
keeping frame 5
writing to /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame5.nii.gz...
mri_convert --frame 6 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame6.nii.gz
mri_convert --frame 6 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame6.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999701, 0.0244268, 0.000465598)
j_ras = (0.023757, 0.976382, -0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
keeping frame 6
writing to /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame6.nii.gz...
mri_convert --frame 7 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame7.nii.gz
mri_convert --frame 7 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame7.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999701, 0.0244268, 0.000465598)
j_ras = (0.023757, 0.976382, -0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
keeping frame 7
writing to /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame7.nii.gz...
mri_convert --frame 8 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame8.nii.gz
mri_convert --frame 8 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame8.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999701, 0.0244268, 0.000465598)
j_ras = (0.023757, 0.976382, -0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
keeping frame 8
writing to /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame8.nii.gz...
mri_convert --frame 9 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame9.nii.gz
mri_convert --frame 9 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame9.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999701, 0.0244268, 0.000465598)
j_ras = (0.023757, 0.976382, -0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
keeping frame 9
writing to /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame9.nii.gz...
mri_concat --i /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame0.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame1.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame2.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame3.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame4.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame5.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame6.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame7.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame8.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi_frame9.nii.gz --mean --o /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/lowb.nii.gz
ninputs = 10
Checking inputs
nframestot = 10
Allocing output
Done allocing
nframes = 10
Computing mean across frames
Writing to /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/lowb.nii.gz
bet /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/lowb.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/lowb_brain.nii.gz -m -f 0.3
mv -f /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/lowb_brain_mask.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/diff
#-------------------------------------
#@# Inter-subject registration Sat Dec 17 16:36:57 CET 2016
flirt -in /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/lowb_brain.nii.gz -ref /aramis/Software/Ubuntu14.04/FSL/fsl-5.0.9-centos5_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/lowb_brain_mni.nii.gz -omat /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/xfms/diff2mni.mat -cost corratio
convert_xfm -omat /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/xfms/mni2diff.mat -inverse /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/xfms/diff2mni.mat
#-------------------------------------
#@# Masks Sat Dec 17 16:37:24 CET 2016
ln -sf /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/diff/lowb_brain_mask.nii.gz /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/nodif_brain_mask.nii.gz
#-------------------------------------
#@# Tensor fit Sat Dec 17 16:37:24 CET 2016
dtifit -k /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dwi.nii.gz -m /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/diff/lowb_brain_mask.nii.gz -r /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/bvecs -b /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/bvals -o /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dtifit
0 128 0 128 0 60
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
44 slices processed
45 slices processed
46 slices processed
47 slices processed
48 slices processed
49 slices processed
50 slices processed
51 slices processed
52 slices processed
53 slices processed
54 slices processed
55 slices processed
56 slices processed
57 slices processed
58 slices processed
59 slices processed
#-------------------------------------
#@# Priors Sat Dec 17 16:37:33 CET 2016
/aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/dmri_train --outdir /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/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.elmo.2005.25745.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 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dtifit_FA.nii.gz --cptdir /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/diff --reg /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/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: /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni
cwd /aramis/dataARAMIS/users/junhao.wen/dataset/Freesurfer/tutorial_data_new/diffusion_tutorial
cmdline /aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/dmri_train --outdir /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/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.elmo.2005.25745.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 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dtifit_FA.nii.gz --cptdir /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/diff --reg /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/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 DELLEED1
machine x86_64
user wen
Output directory: /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni
Output directory in test subject's space: /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/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.elmo.2005.25745.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 DELLEED1 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun 29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Sat Dec 17 16:37:34 CET 2016
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