External Email - Use Caution
Dear FreeSurfer Developers,
I'm attempting to run Tracula using our subjects DTI nifti files on Freesurfer
version 7.1.1 (Ubuntu 18.04).
I could run all steps of "trac-all" commands in a single subject using the
attached configuration file (dmrirc_MULhos554s).
However, I failed to analyze subjects group using the attached another
configuration file (dmrirc_edit).
After "trac-all -prep -c dmrirc_edit" command, I always got a same error
message written below.
sakurai@ubuntu:~/Desktop/freesurfer/tracall$ trac-all -prep -c dmrirc_edit
ERROR: must specify as many fieldmap magnitude dicoms as subjects
I have checked the mail archives and tried to troubleshoot.But I could not find
an adequate solution because of a shortage of knowledges to make appropriate
configuration files.
Please tell me how to make an appropriate configuration file.
Best regards,
Keita SakuraiDepartment of RadiologyNational Center for Geriatrics and
Gerontology
****************************************Keita Sakurai
E-mail: [email protected] of RadiologyNational Center for
Geriatrics and Gerontology7-430 Morioka-cho, Obu, 474-8511, Aichi, Japan
#
# dmrirc.practice
#
# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#
setenv SUBJECTS_DIR /home/sakurai/Desktop/freesurfer/subjects
# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /home/sakurai/Desktop/freesurfer/subjects
# Subject IDs
#
set subjlist = (MULhos554s)
# Default: Run analysis on all subjects
#
set runlist = (1)
# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then the gradient table and b-value table must be specified (see below)
#
set dcmroot = /home/sakurai/Desktop/freesurfer/tracall
set dcmlist = (MULhos554s.nii)
# Diffusion gradient tables (if there is a different one for each scan)
# Must be specified if they cannot be read from the DICOM headers
# The tables must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bveclist = (/home/sakurai/Desktop/freesurfer/tracall/MULhos554s.bvec)
# Diffusion gradient table (if using the same one for all scans)
# Must be specified if it cannot be read from the DICOM headers
# The table must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bvecfile = /home/sakurai/Desktop/freesurfer/tracall/MULhos554s.bvec
# Diffusion b-value tables (if there is a different one for each scan)
# Must be specified if they cannot be read from the DICOM headers
# There must be as many b-values as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bvallist = (/home/sakurai/Desktop/freesurfer/tracall/MULhos554s.bval)
# Diffusion b-value table (if using the same one for all scans)
# Must be specified if it cannot be read from the DICOM headers
# There must be as many b-values as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bvalfile = /home/sakurai/Desktop/freesurfer/tracall/MULhos554s.bval
# Perform registration-based B0-inhomogeneity compensation?
# Default: 0 (no)
#
set dob0 = 0
# Input B0 field map magnitude DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
set b0mlist = None
# Input B0 field map phase DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
set b0plist = None
# Echo spacing for field mapping sequence (from sequence printout)
# Only used if dob0 = 1
# Default: None
#
set echospacing = None
# Perform registration-based eddy-current compensation?
# Default: 1 (yes)
#
set doeddy = 1
# Rotate diffusion gradient vectors to match eddy-current compensation?
# Only used if doeddy = 1
# Default: 1 (yes)
#
set dorotbvecs = 1
# Fractional intensity threshold for BET mask extraction from low-b images
# This mask is used only if usemaskanat = 0
# Default: 0.3
#
set thrbet = 0.3
# Perform diffusion-to-T1 registration by flirt?
# Default: 0 (no)
#
set doregflt = 0
# Perform diffusion-to-T1 registration by bbregister?
# Default: 1 (yes)
#
set doregbbr = 1
# Perform registration of T1 to MNI template?
# Default: 1 (yes)
#
set doregmni = 1
# MNI template
# Only used if doregmni = 1
# Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
#
set mnitemp = /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz
# Perform registration of T1 to CVS template?
# Default: 0 (no)
#
set doregcvs = 0
# Use brain mask extracted from T1 image instead of low-b diffusion image?
# Has no effect if there is no T1 data
# Default: 1 (yes)
#
set usemaskanat = 1
# Paths to reconstruct
# Default: All paths in the atlas
#
set pathlist = ( lh.cst_AS rh.cst_AS \
lh.unc_AS rh.unc_AS \
lh.ilf_AS rh.ilf_AS \
fmajor_PP fminor_PP \
lh.atr_PP rh.atr_PP \
lh.ccg_PP rh.ccg_PP \
lh.cab_PP rh.cab_PP \
lh.slfp_PP rh.slfp_PP \
lh.slft_PP rh.slft_PP )
# Number of path control points
# It can be a single number for all paths or a different number for each of the
# paths specified in pathlist
# Default: 7 for the forceps major, 6 for the corticospinal tract,
# 4 for the angular bundle, and 5 for all other paths
#
set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)
# List of training subjects
# This text file lists the locations of training subject directories
# Default: $FREESURFER_HOME/trctrain/trainlist.txt
#
set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt
# Number of "sticks" (anisotropic diffusion compartments) in the bedpostx
# ball-and-stick model
# Default: 2
#
set nstick = 2
# Number of MCMC burn-in iterations
# (Path samples drawn initially by MCMC algorithm and discarded)
# Default: 200
#
set nburnin = 200
# Number of MCMC iterations
# (Path samples drawn by MCMC algorithm and used to estimate path distribution)
# Default: 7500
#
set nsample = 7500
# Frequency with which MCMC path samples are retained for path distribution
# Default: 5 (keep every 5th sample)
#
set nkeep = 5
# Reinitialize path reconstruction?
# This is an option of last resort, to be used only if one of the reconstructed
# pathway distributions looks like a single curve. This is a sign that the
# initial guess for the pathway was problematic, perhaps due to poor alignment
# between the individual and the atlas. Setting the reinit parameter to 1 and
# rerunning "trac-all -prior" and "trac-all -path", only for the specific
# subjects and pathways that had this problem, will attempt to reconstruct them
# with a different initial guess.
# Default: 0 (do not reinitialize)
#
set reinit = 0
Mon Sep 28 12:40:24 JST 2020
/home/sakurai/Desktop/freesurfer/tracall
/usr/local/freesurfer/bin/trac-all
-bedp -c dmrirc_edit
Subject MULhos554s
SUBJECTS_DIR /home/sakurai/Desktop/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
sakurai
ubuntu
Linux ubuntu 5.4.0-48-generic #52~18.04.1-Ubuntu SMP Thu Sep 10 12:50:22 UTC
2020 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 16384 kbytes
maxproc 63758
maxlocks unlimited
maxsignal 63758
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 16370132 1565124 11136864 36336 3668144 14430548
Swap: 2097148 0 2097148
########################################
Program versions:
trac-all 7.1.1
mri_convert --all-info
ProgramName: mri_convert ProgramArguments: mri_convert --all-info
ProgramVersion: 7.1.1 TimeStamp: 2020/09/28-03:40:24-GMT BuildTime: Jul 23
2020 13:43:33 BuildStamp:
freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: sakurai Machine:
ubuntu Platform: Linux PlatformVersion: 5.4.0-48-generic CompilerName: GCC
CompilerVersion: 4.9.2
FLIRT version 6.0
bbregister 7.1.1
mri_cvs_register 7.1.1
ProgramName: dmri_motion ProgramArguments:
/usr/local/freesurfer/bin/dmri_motion --all-info ProgramVersion: 7.1.1
TimeStamp: 2020/09/28-03:40:24-GMT BuildTime: Jul 23 2020 13:43:33
BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User:
sakurai Machine: ubuntu Platform: Linux PlatformVersion: 5.4.0-48-generic
CompilerName: GCC CompilerVersion: 4.9.2
ProgramName: dmri_train ProgramArguments: /usr/local/freesurfer/bin/dmri_train
--all-info ProgramVersion: 7.1.1 TimeStamp: 2020/09/28-03:40:24-GMT
BuildTime: Jul 23 2020 13:43:33 BuildStamp:
freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: sakurai Machine:
ubuntu Platform: Linux PlatformVersion: 5.4.0-48-generic CompilerName: GCC
CompilerVersion: 4.9.2
ProgramName: dmri_paths ProgramArguments: /usr/local/freesurfer/bin/dmri_paths
--all-info ProgramVersion: 7.1.1 TimeStamp: 2020/09/28-03:40:24-GMT
BuildTime: Jul 23 2020 13:43:33 BuildStamp:
freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: sakurai Machine:
ubuntu Platform: Linux PlatformVersion: 5.4.0-48-generic CompilerName: GCC
CompilerVersion: 4.9.2
ProgramName: dmri_pathstats ProgramArguments:
/usr/local/freesurfer/bin/dmri_pathstats --all-info ProgramVersion: 7.1.1
TimeStamp: 2020/09/28-03:40:24-GMT BuildTime: Jul 23 2020 13:43:33
BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User:
sakurai Machine: ubuntu Platform: Linux PlatformVersion: 5.4.0-48-generic
CompilerName: GCC CompilerVersion: 4.9.2
ProgramName: dmri_mergepaths ProgramArguments:
/usr/local/freesurfer/bin/dmri_mergepaths --all-info ProgramVersion: 7.1.1
TimeStamp: 2020/09/28-03:40:24-GMT BuildTime: Jul 23 2020 13:43:33
BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User:
sakurai Machine: ubuntu Platform: Linux PlatformVersion: 5.4.0-48-generic
CompilerName: GCC CompilerVersion: 4.9.2
ProgramName: dmri_group ProgramArguments: /usr/local/freesurfer/bin/dmri_group
--all-info ProgramVersion: 7.1.1 TimeStamp: 2020/09/28-03:40:24-GMT
BuildTime: Jul 23 2020 13:43:33 BuildStamp:
freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: sakurai Machine:
ubuntu Platform: Linux PlatformVersion: 5.4.0-48-generic CompilerName: GCC
CompilerVersion: 4.9.2
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 /home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dmri
New invocation of trac-all
Mon Sep 28 12:40:24 JST 2020
/home/sakurai/Desktop/freesurfer/tracall
/usr/local/freesurfer/bin/trac-all
-path -c dmrirc_edit
Subject MULhos554s
SUBJECTS_DIR /home/sakurai/Desktop/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
sakurai
ubuntu
Linux ubuntu 5.4.0-48-generic #52~18.04.1-Ubuntu SMP Thu Sep 10 12:50:22 UTC
2020 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 16384 kbytes
maxproc 63758
maxlocks unlimited
maxsignal 63758
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 16370132 1565452 11136536 36336 3668144 14430220
Swap: 2097148 0 2097148
########################################
Program versions:
trac-all 7.1.1
mri_convert --all-info
ProgramName: mri_convert ProgramArguments: mri_convert --all-info
ProgramVersion: 7.1.1 TimeStamp: 2020/09/28-03:40:24-GMT BuildTime: Jul 23
2020 13:43:33 BuildStamp:
freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: sakurai Machine:
ubuntu Platform: Linux PlatformVersion: 5.4.0-48-generic CompilerName: GCC
CompilerVersion: 4.9.2
FLIRT version 6.0
bbregister 7.1.1
mri_cvs_register 7.1.1
ProgramName: dmri_motion ProgramArguments:
/usr/local/freesurfer/bin/dmri_motion --all-info ProgramVersion: 7.1.1
TimeStamp: 2020/09/28-03:40:24-GMT BuildTime: Jul 23 2020 13:43:33
BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User:
sakurai Machine: ubuntu Platform: Linux PlatformVersion: 5.4.0-48-generic
CompilerName: GCC CompilerVersion: 4.9.2
ProgramName: dmri_train ProgramArguments: /usr/local/freesurfer/bin/dmri_train
--all-info ProgramVersion: 7.1.1 TimeStamp: 2020/09/28-03:40:24-GMT
BuildTime: Jul 23 2020 13:43:33 BuildStamp:
freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: sakurai Machine:
ubuntu Platform: Linux PlatformVersion: 5.4.0-48-generic CompilerName: GCC
CompilerVersion: 4.9.2
ProgramName: dmri_paths ProgramArguments: /usr/local/freesurfer/bin/dmri_paths
--all-info ProgramVersion: 7.1.1 TimeStamp: 2020/09/28-03:40:24-GMT
BuildTime: Jul 23 2020 13:43:33 BuildStamp:
freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: sakurai Machine:
ubuntu Platform: Linux PlatformVersion: 5.4.0-48-generic CompilerName: GCC
CompilerVersion: 4.9.2
ProgramName: dmri_pathstats ProgramArguments:
/usr/local/freesurfer/bin/dmri_pathstats --all-info ProgramVersion: 7.1.1
TimeStamp: 2020/09/28-03:40:24-GMT BuildTime: Jul 23 2020 13:43:33
BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User:
sakurai Machine: ubuntu Platform: Linux PlatformVersion: 5.4.0-48-generic
CompilerName: GCC CompilerVersion: 4.9.2
ProgramName: dmri_mergepaths ProgramArguments:
/usr/local/freesurfer/bin/dmri_mergepaths --all-info ProgramVersion: 7.1.1
TimeStamp: 2020/09/28-03:40:24-GMT BuildTime: Jul 23 2020 13:43:33
BuildStamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User:
sakurai Machine: ubuntu Platform: Linux PlatformVersion: 5.4.0-48-generic
CompilerName: GCC CompilerVersion: 4.9.2
ProgramName: dmri_group ProgramArguments: /usr/local/freesurfer/bin/dmri_group
--all-info ProgramVersion: 7.1.1 TimeStamp: 2020/09/28-03:40:24-GMT
BuildTime: Jul 23 2020 13:43:33 BuildStamp:
freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 User: sakurai Machine:
ubuntu Platform: Linux PlatformVersion: 5.4.0-48-generic CompilerName: GCC
CompilerVersion: 4.9.2
New invocation of trac-paths
sakurai
ubuntu
Linux ubuntu 5.4.0-48-generic #52~18.04.1-Ubuntu SMP Thu Sep 10 12:50:22 UTC
2020 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 16384 kbytes
maxproc 63758
maxlocks unlimited
maxsignal 63758
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 16370132 1566484 11135504 36336 3668144 14429188
Swap: 2097148 0 2097148
#-------------------------------------
/usr/local/freesurfer/bin/trac-paths
#-------------------------------------
#@# Path reconstruction Mon Sep 28 12:40:24 JST 2020
rm -rf
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/lh.cst_AS_avg33_mni_bbr
rm -rf
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/rh.cst_AS_avg33_mni_bbr
rm -rf
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/lh.unc_AS_avg33_mni_bbr
rm -rf
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/rh.unc_AS_avg33_mni_bbr
rm -rf
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/lh.ilf_AS_avg33_mni_bbr
rm -rf
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/rh.ilf_AS_avg33_mni_bbr
rm -rf
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/fmajor_PP_avg33_mni_bbr
rm -rf
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/fminor_PP_avg33_mni_bbr
rm -rf
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/lh.atr_PP_avg33_mni_bbr
rm -rf
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/rh.atr_PP_avg33_mni_bbr
rm -rf
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/lh.ccg_PP_avg33_mni_bbr
rm -rf
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/rh.ccg_PP_avg33_mni_bbr
rm -rf
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/lh.cab_PP_avg33_mni_bbr
rm -rf
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/rh.cab_PP_avg33_mni_bbr
rm -rf
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/lh.slfp_PP_avg33_mni_bbr
rm -rf
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/rh.slfp_PP_avg33_mni_bbr
rm -rf
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/lh.slft_PP_avg33_mni_bbr
rm -rf
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/rh.slft_PP_avg33_mni_bbr
/usr/local/freesurfer/bin/dmri_paths --outdir
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/lh.cst_AS_avg33_mni_bbr
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/rh.cst_AS_avg33_mni_bbr
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/lh.unc_AS_avg33_mni_bbr
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/rh.unc_AS_avg33_mni_bbr
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/lh.ilf_AS_avg33_mni_bbr
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/rh.ilf_AS_avg33_mni_bbr
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/fmajor_PP_avg33_mni_bbr
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/fminor_PP_avg33_mni_bbr
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/lh.atr_PP_avg33_mni_bbr
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/rh.atr_PP_avg33_mni_bbr
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/lh.ccg_PP_avg33_mni_bbr
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/rh.ccg_PP_avg33_mni_bbr
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/lh.cab_PP_avg33_mni_bbr
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/rh.cab_PP_avg33_mni_bbr
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/lh.slfp_PP_avg33_mni_bbr
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/rh.slfp_PP_avg33_mni_bbr
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/lh.slft_PP_avg33_mni_bbr
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dpath/rh.slft_PP_avg33_mni_bbr
--dwi /home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dmri/dwi.nii.gz
--grad /home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dmri/bvecs --bval
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dmri/bvals --mask
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/lowb_brain_mask.nii.gz
--bpdir /home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dmri.bedpostX
--ntr 2 --fmin 0.05 --roi1
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz
--roi2
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/fmajor_PP_avg33_mni_bbr_end2_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/fminor_PP_avg33_mni_bbr_end2_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz
--reg
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dmri/xfms/diff2mni.bbr.mat
--init
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_5.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_5.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_4.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_4.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5.txt
--nprior
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnids_all
--lprior
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/fminor_PP_avg33_mni_bbr_fsprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/fminor_PP_avg33_mni_bbr_fsids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior_all
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids_all
--seg
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/mni/aparc+aseg.nii.gz
--nb 200 --ns 7500 --nu 0 --nk 5 --sdp
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_4_std.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_4_std.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt
/home/sakurai/Desktop/freesurfer/subjects/MULhos554s/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt
Linux ubuntu 5.4.0-48-generic #52~18.04.1-Ubuntu SMP Thu Sep 10 12:50:22 UTC
2020 x86_64 x86_64 x86_64 GNU/Linux
trac-paths exited with ERRORS at Mon Sep 28 12:40:25 JST 2020
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