hello experts.
i have some question to you...
when i enter the recon-all -i /paht~
error showed up.... like below one..
how can i to fix it?
[areum@localhost 0165766_1]# recon-all -i
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm -all -s sub002
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects/OSA/0165766_1
Actual FREESURFER_HOME /usr/local/freesurfer
Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16
UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm...
Starting DICOMRead2()
dcmfile = /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm
dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1
Ref Series No = 3
Found 247 files, checking for dicoms
Found 244 dicom files in series.
First Sorting
Computing Slice Direction
Vs: -0.8 0 0
Vs: -1 0 0
Second Sorting
Counting frames
nframes = 1
nslices = 244
ndcmfiles = 244
PE Dir = ROW (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2.1--
Loading pixel data
TR=7.70, TE=3.37, TI=400.00, flip angle=12.00
i_ras = (0, -1, 0)
j_ras = (0, 0, -1)
k_ras = (1, -0, 0)
writing to
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz...
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm...
Starting DICOMRead2()
dcmfile = /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm
dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1
Ref Series No = 3
Found 247 files, checking for dicoms
Found 244 dicom files in series.
First Sorting
Computing Slice Direction
Vs: -0.8 0 0
Vs: -1 0 0
Second Sorting
Counting frames
nframes = 1
nslices = 244
ndcmfiles = 244
PE Dir = ROW (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2.1--
Loading pixel data
TR=7.70, TE=3.37, TI=400.00, flip angle=12.00
i_ras = (0, -1, 0)
j_ras = (0, 0, -1)
k_ras = (1, -0, 0)
writing to
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz...
#--------------------------------------------
#@# MotionCor Thu Nov 5 02:27:17 PST 2015
Found 2 runs
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
Checking for (invalid) multi-frame inputs...
Checking for (invalid) multi-frame inputs...
#-----------------------------------------------
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002
mri_robust_template --mov
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
--average 1 --template
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz --satit
--inittp 1 --fixtp --noit --iscale
--iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001-iscale.txt
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.txt
--subsample 200 --lta
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
--mov: Using
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz as
movable/source volume.
--mov: Using
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz as
movable/source volume.
Total: 2 input volumes
--average: Using method 1 for template computation.
--template: Using
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz as
template output volume.
--satit: Will estimate SAT iteratively!
--inittp: Using TP 1 as target for initialization
--fixtp: Will map everything to init TP!
--noit: Will output only first template (no iterations)!
--iscale: Enableing intensity scaling!
--iscaleout: Will perform intensity scaling and output results
--subsample: Will subsample if size is larger than 200 on all axes!
--lta: Will output LTA transforms
reading source
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'...
converting source
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' to
bspline ...
MRItoBSpline degree 3
reading source
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'...
converting source
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' to
bspline ...
MRItoBSpline degree 3
MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 ,
epsit 0.01 ) :
[init] ========================= TP 2 to TP 1 ==============================
Register TP 2 (
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz )
to TP 1 (
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz )
-- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244)
voxels.
-- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417)
voxels.
-- Reslicing using cubic bspline
MRItoBSpline degree 3
-- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244)
voxels.
-- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417)
voxels.
-- Reslicing using cubic bspline
MRItoBSpline degree 3
- Max Resolution used: 3
-- gpS ( 64 , 64 , 52 )
-- gpT ( 64 , 64 , 52 )
- running loop to estimate saturation parameter:
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Killed
Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16
UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub002 exited with ERRORS at Thu Nov 5 02:37:57 PST 2015
For more details, see the log file
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
2015-10-19 11:05 GMT+09:00 A-reum Min <naniy...@gmail.com>:
hello experts.
i have a question to you..
i'm doing recon-all stage, but errors show up like this
ects/OSA/14/subj014/mri/orig/002.mgz --average 1 --template
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz --satit
--inittp 1 --fixtp --noit --iscale --iscaleout
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt
--subsample 200 --lta
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta
/
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter
Exp $
--mov: Using
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as
movable/source volume.
--mov: Using
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz as
movable/source volume.
Total: 2 input volumes
--average: Using method 1 for template computation.
--template: Using
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz as
template output volume.
--satit: Will estimate SAT iteratively!
--inittp: Using TP 1 as target for initialization
--fixtp: Will map everything to init TP!
--noit: Will output only first template (no iterations)!
--iscale: Enableing intensity scaling!
--iscaleout: Will perform intensity scaling and output results
--subsample: Will subsample if size is larger than 200 on all axes!
--lta: Will output LTA transforms
reading source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
converting source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to
bspline ...
MRItoBSpline degree 3
reading source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'...
converting source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' to
bspline ...
MRItoBSpline degree 3
MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5
, epsit 0.01 ) :
[init] ========================= TP 2 to TP 1
==============================
Register TP 2 (
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz )
to TP 1 (
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz )
-- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512,
244) voxels.
-- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512,
417) voxels.
-- Reslicing using cubic bspline
MRItoBSpline degree 3
-- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512,
244) voxels.
-- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512,
417) voxels.
-- Reslicing using cubic bspline
MRItoBSpline degree 3
- Max Resolution used: 3
-- gpS ( 64 , 64 , 52 )
-- gpT ( 64 , 64 , 52 )
- running loop to estimate saturation parameter:
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Killed
[areum@localhost 14]#
[areum@localhost 14]# $Id: mri_robust_template.cpp,v 1.37.2.2
2012/10/10 19:59:06 mreuter Exp $
c
Bad : modifier in $ ( ).
[areum@localhost 14]#
[areum@localhost 14]# --mov: Using
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as
movable/source volume.
--mov:: Too many arguments.
[areum@localhost 14]# --mov: Using
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz as
movable/source volume.
--mov:: Too many arguments.
[areum@localhost 14]# Total: 2 input volumes
Total:: Too many arguments.
b
[areum@localhost 14]# --average: Using method 1 for template
computation.
--average:: Too many arguments.
[areum@localhost 14]# --template: Using
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz as
template output volume.
--template:: Too many arguments.
[areum@localhost 14]# --satit: Will estimate SAT iteratively!
i
--satit:: Too many arguments.
[areum@localhost 14]# --inittp: Using TP 1 as target for
initialization
--inittp:: Too many arguments.
[areum@localhost 14]# --fixtp: Will map everything to init TP!
--fixtp:: Too many arguments.
[areum@localhost 14]# --noit: Will output only first template (no
iterations)!
Badly placed ()'s.
[areum@localhost 14]# --iscale: Enableing intensity scaling!
--iscale:: Too many arguments.
[areum@localhost 14]# --iscaleout: Will perform intensity scaling and
output results
--iscaleout:: Too many arguments.
[areum@localhost 14]# --subsample: Will subsample if size is larger
than 200 on all axes!
--subsample:: Too many arguments.
[areum@localhost 14]# --lta: Will output LTA transforms
--lta:: Too many arguments.
[areum@localhost 14]# reading source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
-
reading: Command not found.
[areum@localhost 14]# converting source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to
bspline ...
b
converting: Command not found.
[areum@localhost 14]# MRItoBSpline degree 3
r
MRItoBSpline: Command not found.
[areum@localhost 14]# reading source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'...
n
reading: Command not found.
[areum@localhost 14]# converting source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' to
bspline ...
converting: Command not found.
[areum@localhost 14]# MRItoBSpline degree 3
p
MRItoBSpline: Command not found.
[areum@localhost 14]#
[areum@localhost 14]# MultiRegistration::initializing Xforms (init 1 ,
maxres 0 , iterate 5 , epsit 0.01 ) :
/
Badly placed ()'s.
[areum@localhost 14]#
[areum@localhost 14]# [init] ========================= TP 2 to TP 1
==============================
a
[init]: No match.
[areum@localhost 14]# Register TP 2 (
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz )
Badly placed ()'s.
e
[areum@localhost 14]# to TP 1 (
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz )
n
Badly placed ()'s.
[areum@localhost 14]#
[areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001)
mm size and (512, 512, 244) voxels.
Badly placed (.
[areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm
size and (512, 512, 417) voxels.
Badly placed (.
[areum@localhost 14]# -- Reslicing using cubic bspline
a
--: Command not found.
[areum@localhost 14]# MRItoBSpline degree 3
T
MRItoBSpline: Command not found.
[areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001)
mm size and (512, 512, 244) voxels.
Badly placed (.
[areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm
size and (512, 512, 417) voxels.
Badly placed (.
[areum@localhost 14]# -- Reslicing using cubic bspline
a
--: Command not found.
[areum@localhost 14]# MRItoBSpline degree 3
u
MRItoBSpline: Command not found.
[areum@localhost 14]#
[areum@localhost 14]# - Max Resolution used: 3
i
-: Command not found.
[areum@localhost 14]# -- gpS ( 64 , 64 , 52 )
Badly placed ()'s.
[areum@localhost 14]# -- gpT ( 64 , 64 , 52 )
Badly placed ()'s.
[areum@localhost 14]# - running loop to estimate saturation
parameter:
l
-: Command not found.
[areum@localhost 14]# Sigma too small: 0 (identical images?)
Badly placed ()'s.
[areum@localhost 14]# Sigma too small: 0 (identical images?)
Badly placed ()'s.
[areum@localhost 14]# Sigma too small: 0 (identical images?)
Badly placed ()'s.
[areum@localhost 14]# Sigma too small: 0 (identical images?)
Badly placed ()'s.
[areum@localhost 14]# Sigma too small: 0 (identical images?)
Badly placed ()'s.
[areum@localhost 14]# Sigma too small: 0 (identical images?)
Badly placed ()'s.
4
[areum@localhost 14]# Sigma too small: 0 (identical images?)
Badly placed ()'s.
[areum@localhost 14]# Sigma too small: 0 (identical images?)
Badly placed ()'s.
[areum@localhost 14]# Sigma too small: 0 (identical images?)
Badly placed ()'s.
[areum@localhost 14]# Sigma too small: 0 (identical images?)
Badly placed ()'s.
[areum@localhost 14]# Killed
.
Killed: Command not found.
[areum@localhost 14]# Linux localhost.localdomain
2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64
x86_64 x86_64 GNU/Linux
Linux: Command not found.
[areum@localhost 14]#
[areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat
Oct 17 07:50:15 PDT 2015
a
ERROR: Flag exited unrecognized.
-s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015
Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15
04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:33 PDT
2015
For more details, see the log file
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
[areum@localhost 14]#
[areum@localhost 14]# For more details, see the log file
/usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log
For: Command not found.
[areum@localhost 14]# To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
e
To: Command not found.
[areum@localhost 14]#
[areum@localhost 14]# [areum@localhost 14]# recon-all -i
/usr/local/freesurfer/subjects/OSA/14/I0000001.dcm -i /usr/local/
[areum@localhost: Command not found.
[areum@localhost 14]# Subject Stamp: freesurfer-Linux-centos6_x86_6
i
Subject: Command not found.
[areum@localhost 14]# Current Stamp: freesurfer-Linux-centos6_x8
2
Current: Command not found.
[areum@localhost 14]# INFO: SUBJEC
INFO:: Too many arguments.
[areum@localhost 14]# Actual FREESURFER_HOME /usr/local/freesurfer
8
Actual: Command not found.
[areum@localhost 14]# Linux localhost.l
s
Linux: Command not found.
[areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014
g
/usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied.
[areum@localhost 14]#
[areum@localhost 14]# mri_convert /u
mri_convert /u
mri_convert: missing output volume name
type mri_convert -u for usage
[areum@localhost 14]#
[areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/
mri_convert /usr/local/freesurfer/subjects/
mri_convert: missing output volume name
type mri_convert -u for usage
[areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05
21:55:16 mreuter Exp $
Bad : modifier in $ ( ).
[areum@localhost 14]# reading from
/usr/local/freesurfer/subjects/OSA/14/I0000001.dcm...
reading: Command not found.
[areum@localhost 14]# Startin
Startin: Command not found.
[areum@localhost 14]# dcmfile =
/usr/local/freesurfer/subjects/OSA/14/I0000001.dcm
dcmfile: Command not found.
[areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14
dcmdir: Command not found.
[areum@localhost 14]# Ref Series No = 3
Ref: Command not found.
[areum@localhost 14]# Found 247 files, checking for dicoms
Found: Command not found.
[areum@localhost 14]# Found 244 dicom files in series.
Found: Command not found.
[areum@localhost 14]# First Sorting
First: Command not found.
[areum@localhost 14]# Computing Slice Direction
Computing: Command not found.
[areum@localhost 14]# Vs: -0.8 0 0
Vs:: Too many arguments.
[areum@localhost 14]# Vs: -1 0 0
Vs:: Too many arguments.
[areum@localhost 14]# Second Sorting
Second: Command not found.
[areum@localhost 14]# Counting frames
Counting: Command not found.
[areum@localhost 14]# nframes = 1
nframes: Command not found.
[areum@localhost 14]# nslices = 244
nslices: Command not found.
[areum@localhost 14]# ndcmfiles = 244
ndcmfiles: Command not found.
[areum@localhost 14]# PE Dir = ROW (dicom read)
Badly placed ()'s.
[areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1--
TransferSyntaxUID:: Too many arguments.
[areum@localhost 14]# Loading pixel data
Loading: Command not found.
[areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00
TR=7.70,: Command not found.
[areum@localhost 14]# i_ras = (0, -1, 0)
Badly placed ()'s.
[areum@localhost 14]# j_ras = (0, 0, -1)
Badly placed ()'s.
[areum@localhost 14]# k_ras = (1, -0, 0)
Badly placed ()'s.
[areum@localhost 14]# writing to
/usr/local/freesurfer/subjects/OSA/14/subj014/
writing: Command not found.
[areum@localhost 14]#
[areum@localhost 14]#
[areum@localhost 14]# mri_convert
/usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/loc
mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
/usr/loc
mri_convert: can't determine type of output volume
[areum@localhost 14]#
[areum@localhost 14]# mri_convert
/usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm...
Starting DICOMRead2()
dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
dcmdir = /usr/local/freesurfer/subjects/OSA/14
Ref Series No = 3
Found 247 files, checking for dicoms
Found 244 dicom files in series.
First Sorting
Computing Slice Direction
Vs: -0.8 0 0
Vs: -1 0 0
Second Sorting
Counting frames
nframes = 1
nslices = 244
ndcmfiles = 244
PE Dir = ROW (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2.1--
Loading pixel data
TR=7.70, TE=3.37, TI=400.00, flip angle=12.00
i_ras = (0, -1, 0)
j_ras = (0, 0, -1)
k_ras = (1, -0, 0)
writing to
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz...
[areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05
21:55:16 mreuter Exp $
Bad : modifier in $ ( ).
[areum@localhost 14]# reading from /usr/local/freesurfer/sub
reading: Command not found.
[areum@localhost 14]# Starting DICOMRead2()
Badly placed ()'s.
[areum@localhost 14]# dcmfile =
/usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
dcmfile: Command not found.
[areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14
dcmdir: Command not found.
[areum@localhost 14]# Ref Series No = 3
Ref: Command not found.
[areum@localhost 14]# Found 247 files, checking for dicoms
Found: Command not found.
[areum@localhost 14]# Found 244 di
Found: Command not found.
[areum@localhost 14]# First Sorting
First: Command not found.
[areum@localhost 14]# Computing Slice Direction
Computing: Command not found.
[areum@localhost 14]# Vs: -0.8 0 0
Vs:: Too many arguments.
[areum@localhost 14]# Vs: -1 0 0
Vs:: Too many arguments.
[areum@localhost 14]# Second Sorting
Second: Command not found.
[areum@localhost 14]# Counting frames
Counting: Command not found.
[areum@localhost 14]# nframes = 1
nframes: Command not found.
[areum@localhost 14]# nslices = 244
nslices: Command not found.
[areum@localhost 14]# ndcmfiles = 244
ndcmfiles: Command not found.
[areum@localhost 14]# PE Dir = ROW (dicom read)
Badly placed ()'s.
[areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1--
TransferSyntaxUID:: Too many arguments.
[areum@localhost 14]# Loading pixel data
Loading: Command not found.
[areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00
TR=7.70,: Command not found.
[areum@localhost 14]# i_ras = (0, -1, 0)
Badly placed ()'s.
[areum@localhost 14]# j_ras = (0, 0, -1)
Badly placed ()'s.
[areum@localhost 14]# k_ras = (1, -0, 0)
Badly placed ()'s.
[areum@localhost 14]# writing to
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz...
writing: Command not found.
[areum@localhost 14]# #----------------------------
#----------------------------: Command not found.
[areum@localhost 14]# #@# MotionCor Sat Oct 17 08:09:23 PDT 2015
#@#: Command not found.
[areum@localhost 14]# Found 2 runs
Found: Command not found.
[areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/sub
/usr/local/freesurfer/subjects/OSA/14/sub: Command not found.
[areum@localhost 14]# /usr/local/freesurfer
/usr/local/freesurfer: Permission denied.
[areum@localhost 14]# Checking for (invalid) multi-frame inputs...
Badly placed ()'s.
[areum@localhost 14]# Checking for (invalid) multi-frame in
Badly placed ()'s.
[areum@localhost 14]# #-----------------------------------------------
#-----------------------------------------------: Command not found.
[areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014
/usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied.
[areum@localhost 14]#
[areum@localhost 14]#
[areum@localhost 14]#
[areum@localhost 14]# $Id: mri_robust_temp
Bad : modifier in $ ( ).
[areum@localhost 14]#
[areum@localhost 14]# --mov: Using
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as
movable/
--mov:: Too many arguments.
[areum@localhost 14]# --mov: Using
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz a
--mov:: Too many arguments.
[areum@localhost 14]# Total: 2 input volumes
Total:: Too many arguments.
[areum@localhost 14]# --average: Using method 1 for template
computation.
--average:: Too many arguments.
[areum@localhost 14]# --template
--template: Command not found.
[areum@localhost 14]# --satit: Will estimate SAT iteratively!
--satit:: Too many arguments.
[areum@localhost 14]# --inittp: Using TP 1 as target for
initialization
--inittp:: Too many arguments.
[areum@localhost 14]# --fixtp: Will map everything to init TP!
--fixtp:: Too many arguments.
[areum@localhost 14]# --noit: Will output only first template (no
iterations)!
Badly placed ()'s.
[areum@localhost 14]# --iscale: Enableing intensity scaling!
--iscale:: Too many arguments.
[areum@localhost 14]# --iscaleout: Will perform intensity scaling and
output results
--iscaleout:: Too many arguments.
[areum@localhost 14]# --subsa
--subsa: Command not found.
[areum@localhost 14]# --lta: Will output LT
--lta:: Too many arguments.
[areum@localhost 14]# reading source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
reading: Command not found.
[areum@localhost 14]# converting source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to
bspline ...
converting: Command not found.
[areum@localhost 14]# MRItoBSpline degree 3
MRItoBSpline: Command not found.
[areum@localhost 14]# rea
rea: Command not found.
[areum@localhost 14]# converting source '/u
Unmatched '.
[areum@localhost 14]# MRItoBSpline degree 3
MRItoBSpline: Command not found.
[areum@localhost 14]#
[areum@localhost 14]# Multi
Multi: Command not found.
[areum@localhost 14]#
[areum@localhost 14]# [init] ========================= TP 2 to TP 1
==============================
[init]: No match.
[areum@localhost 14]# Register TP 2 ( /usr/l
Too many ('s.
[areum@localhost 14]# to TP 1 (
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz )
Badly placed ()'s.
[areum@localhost 14]#
[areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001)
mm size and (512, 512, 244) voxels.
Badly placed (.
[areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm
size and (512, 512, 4
Too many ('s.
[areum@localhost 14]# -- Reslicing using cubic bspline
--: Command not found.
[areum@localhost 14]# MRItoBSpline degree 3
MRItoBSpline: Command not found.
[areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001)
mm size and (512, 512, 244) voxels.
Badly placed (.
[areum@localhost 14]# -- Resampled: (0.
Too many ('s.
[areum@localhost 14]# -- Reslicing using cubic bspline
--: Command not found.
[areum@localhost 14]# MRItoBSpline degree 3
MRItoBSpline: Command not found.
[areum@localhost 14]#
[areum@localhost 14]# - Max Resolution used: 3
-: Command not found.
[areum@localhost 14]# -- gpS ( 64 , 64 ,
Too many ('s.
[areum@localhost 14]# -- gpT ( 64 , 64 , 52 )
Badly placed ()'s.
[areum@localhost 14]# - running loop to estimate saturation pa
-: Command not found.
[areum@localhost 14]# Sigma too small: 0 (identical images?)
Badly placed ()'s.
[areum@localhost 14]# Sigma too small: 0 (identical images?)
Badly placed ()'s.
[areum@localhost 14]# Sigma too small: 0
Sigma: Command not found.
[areum@localhost 14]# Sigma too small: 0 (identical images?)
Badly placed ()'s.
[areum@localhost 14]# Sigma too small: 0 (identical image
Too many ('s.
[areum@localhost 14]# Sigma too small: 0 (identical images?)
Badly placed ()'s.
[areum@localhost 14]# Sigma too small: 0 (identical images?)
Badly placed ()'s.
[areum@localhost 14]# Sigma too small:
Sigma: Command not found.
[areum@localhost 14]# Sigma too small: 0 (identical images?)
Badly placed ()'s.
[areum@localhost 14]# Si
Si: Command not found.
[areum@localhost 14]# Killed
Killed: Command not found.
[areum@localhost 14]# Linux localhost.localdomain 2.6.32
Linux: Command not found.
[areum@localhost 14]#
[areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat
Oct 17 08
ERROR: Flag exited unrecognized.
-s subj014 exited with ERRORS at Sat Oct 17 08
Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15
04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:53 PDT
2015
For more details, see the log file
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
how can i to do?
plz help me..
2015-10-18 0:11 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:
Hi A-reum
can you please follow the bug-reporting procedures in:
https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
also, don't include a snapshot of text - cutting and
pasting the actual text in is far more useful, but in
addition we need a lot of other information if we are to
be able to help you
cheers
Bruce
On Sun, 18 Oct 2015, A-reum Min wrote:
hello experts.
I have a question to you...
I'm doing recon-all stage... but errors showed up
(fig.1)
how can i to do?
plz, help me
2015-09-16 23:56 GMT+09:00 Douglas Greve
<gr...@nmr.mgh.harvard.edu>:
don't use .hdr. When you have a .hdr/.img
pair, just use the .img file.
On 9/16/15 10:51 AM, A-reum Min wrote:
hello, experts
I have some question.
I want to use analyze format instead of DICOM file.
So, i type this sentence
recon-all -i
/usr/local/freesurfer/subjects/test_han/I0071579.hdr
-i
/usr/local/freesurfer/subjects/test_han/I0071579.img
-all -s han001
and then error occured....
ERROR: cannot determine file type for
/usr/local/freesurfer/subjects/test_han/I0071579.hdr
Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1
SMP Wed Oct 15
04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s han001 exited with ERRORS at Wed Sep 16
06:35:02 PDT 2015
For more details, see the log file
/usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
How can i to do using analyze format?
2015-08-27 23:55 GMT+09:00 Douglas N Greve
<gr...@nmr.mgh.harvard.edu>:
Specify something for --seg. It just needs to
be a surface
overlay of
the same size as the input.
On 08/27/2015 01:49 AM, A-reum Min wrote:
> Hello doug
>
> i enter the ' mri_segstats --i y.mgh --vox
33 0 0 --avgwf
out.dat'
> then, error occured --> ERROR: must specify
a segmentation
volume
>
>
> 2015-08-27 12:50 GMT+09:00 Douglas Greve
<gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>:
>
> don't use "vertexno", just put the
vertex number, eg,
--vox 33 0 0
>
>
> On 8/26/15 9:22 PM, A-reum Min wrote:
>> Hello developer,
>>
>> I have some question to you.
>>
>> How can i get the significant vertices
value using Qdec
result?
>>
>> When i enter the 'mri_segstats --i
y.mgh --vox vertexno
33 0 0
>> --avgwf out.dat', then error ouccured
--> ERROR :
Option out.dat
>> unknown.
>>
>> So, i enter the 'mri_segstats --i y.mgh
--vox vertexno
33 0 0
>> --avgwf out.dat', then error occured
--> ERROR : Option
0 unkown.
>>
>> How can i fix it?
>>
>>
>>
>>
>>
>>
>>
>> 2015-08-25 23:41 GMT+09:00 Douglas
Greve
>> <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>:
>>
>>
>>
>> On 8/25/15 9:35 AM, A-reum Min
wrote:
>>> Hello developers
>>>
>>> I have some question to you.
>>>
>>> 1.In fig.png, how many vertices
were composed of
cluster at
>>> least?
>> I'm not sure what you mean. it does
not look like
there are
>> any clusters there
>>>
>>> 2. How to change Area
Threshold(fig.png)?
>> The area is controlled by the
clusterwise threshold
(--cwp)
>> to mri_glmfit-sim
>>>
>>> 3. How to change CSD
thresh(fig.png)?
>> That is controlled by the threshold
when specifying
"--cache
>> threshold sign" to mri_glmfit-sim
>>>
>>> 4. What is the difference between
two words(Area
Threshold,
>>> CSD thresh)?
>> One is the cluster-pvalue and the
other is the
>> cluster-forming thershold
>>>
>>> 5. What is the exactly mean two
words(Area
Threshold, CSD
>>> thresh)?
>> See above
>>
>>>
>>> Thank you
>>>
>>> 2015-08-12 23:23 GMT+09:00 Douglas
N Greve
>>> <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>:
>>>
>>>
>>>
>>> On 08/10/2015 10:06 PM, A-reum
Min wrote:
>>> > HI expert !
>>> >
>>> > My name is Areum. I have
some question to
you.
>>> >
>>> > 1. Does FreeSurfer offer a
effect size? if
that offer,
>>> how can i use
>>> > effect size?
>>> >
>>> If you're doing a group
analysis, you can
compute
>>> fscalc
glmdir/contrast/gamma.mgh div
glmdir/rstd.mgh -o
>>> glmdir/contrast/effectsize.mgh
>>> >
>>> > 2. I was wondering about the
stats.dat file
in
>>> stats_table (in Qdec
>>> > folder).
>>> >
>>> > Stats.dat file’s value mean
that each area’s
average
>>> (include whole
>>> > vertex) or each
>>> >
>>> > area’s average (only
significant vertex)?
>>> >
>>> what stats.dat? if
subject/stats/lh.aparc.stats, then
>>> the area is the
>>> total area for the ROI
>>> >
>>> > 3. Can I get whole vertex
value or
significant vertex
>>> value? Because,
>>> > I want to
>>> >
>>> > compare two groups
correlation using SPSS. In
>>> addition, I want to compare
>>> >
>>> > thickness, volume and
surface area
correlation within
>>> the one group
>>> > using SPSS.
>>> >
>>> You can extract a given vertex
with
>>> mri_segstats --i y.mgh --crs
vertexno 0 0
--avgwf
>>> vertexno.dat
>>> vertexno.dat will be a text
file with number of
rows
>>> equalt to thge
>>> number of subjects where the
value is the data
from the
>>> given (0-based)
>>> vertex no. y.mgh is the input
to mri_glmfit
>>> >
>>> > 4. I currently use the
default cluster
>>> size(significant area
threshold
>>> > is 0mm^2). So, I
>>> >
>>> > want to control cluster size
larger than
default
>>> cluster size. How can
>>> > I control the
>>> >
>>> > cluster size?
>>> >
>>> I don't know what you mean.
>>> >
>>> > 5. In FreeSurfer manual, GLM
and Qdec have a
same
>>> results. But when I
>>> > use the
>>> >
>>> > both(GLM, Qdec) group
analysis program
results are not
>>> same. What is
>>> > differences
>>> >
>>> > between two analysis
program? How can I get
same
>>> result while GLM and
>>> > Qdec?
>>> >
>>> No way to know unless you tell
us the specifics
of what
>>> you did
>>> >
>>> > 6. How can I get surface
area and volume
using
>>> GLM(group analysis
>>> > program)?
>>> >
>>> surface area and volume are
outputs of
recon-all, not glm
>>> >
>>> >
>>> > plz reply to me
>>> >
>>> >
>>> > 2015-08-10 21:35 GMT+09:00
A-reum Min
>>> <naniy...@gmail.com
<mailto:naniy...@gmail.com>
>>> > <mailto:naniy...@gmail.com
<mailto:naniy...@gmail.com>>>:
>>> >
>>> > Hello developer~
>>> >
>>> > I have some questions to you.
>>> >
>>> > 1. Does FreeSurfer offer a
effect size? if that
>>> offer, how can i
>>> > use effect size?
>>> >
>>> > 2. I was wondering about the
stats.dat file in
>>> stats_table (in
>>> > Qdec folder).
>>> >
>>> > Stats.dat file’s value mean
that each area’s
>>> average (include
>>> > whole vertex) or each
>>> >
>>> > area’s average (only
significant vertex)?
>>> >
>>> > 3. Can I get whole vertex
value or significant
>>> vertex value?
>>> > Because, I want to
>>> >
>>> > compare two groups correlation
using SPSS. In
>>> addition, I want to
>>> > compare
>>> >
>>> > thickness, volume and surface
area correlation
>>> within the one
>>> > group using SPSS.
>>> >
>>> > 4. I currently use the default
cluster
>>> size(significant area
>>> > threshold is 0mm^2). So, I
>>> >
>>> > want to control cluster size
larger than
default
>>> cluster size. How
>>> > can I control the
>>> >
>>> > cluster size?
>>> >
>>> > 5. In FreeSurfer manual, GLM
and Qdec have a
same
>>> results. But
>>> > when I use the
>>> >
>>> > both(GLM, Qdec) group analysis
program results
are
>>> not same. What
>>> > is differences
>>> >
>>> > between two analysis program?
How can I get
same
>>> result while GLM
>>> > and Qdec?
>>> >
>>> > 6. How can I get surface area
and volume using
>>> GLM(group analysis
>>> > program)?
>>> >
>>> >
>>> > thanks for your help
>>> >
>>> >
>>> > 2015-07-27 14:28 GMT+09:00
A-reum Min
>>> <naniy...@gmail.com
<mailto:naniy...@gmail.com>
>>> > <mailto:naniy...@gmail.com
>>> <mailto:naniy...@gmail.com>>>:
>>> >
>>> > Hello bruce
>>> >
>>> > I solve this
problem(12.png)
>>> >
>>> > Thank you
>>> >
>>> > 2015-07-27 13:03 GMT+09:00
dgw
>>> <dgwake...@gmail.com
<mailto:dgwake...@gmail.com>
>>> >
<mailto:dgwake...@gmail.com
>>> <mailto:dgwake...@gmail.com>>>:
>>> >
>>> > Hi A-reum,
>>> >
>>> > I think you may be
able to get a faster
>>> response if you
>>> > include some
>>> > details about your
setup: I would start
>>> with the following:
>>> >
>>> >
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> > and run bugr.
>>> >
>>> > hth
>>> > D
>>> >
>>> > On 7/26/15 5:17 PM,
A-reum Min wrote:
>>> > > Hi, Bruce
>>> > >
>>> > > When i use a Qdec,
this
message(12.png)
>>> show up..
>>> > > How can i solve this
problem?
>>> > >
>>> > > 2015-07-23 22:57
GMT+09:00 Bruce
Fischl
>>> >
<fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>
>>> >
<mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>>
>>> > >
<mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>
>>> >
<mailto:fis...@nmr.mgh.harvard.edu
>>>
<mailto:fis...@nmr.mgh.harvard.edu>>>>:
>>> > >
>>> > > 1. No, each
subject has a
different
>>> #. You can map
>>> > to fsaverage
>>> > > (this is what
-qcache does if you
>>> specify it for
>>> > recon-all), then
>>> > > they will have
the same #.
>>> > >
>>> > > 2. What result
data do you mean?
>>> > >
>>> > > 3. Yes, although
I'll leave the
>>> details to Doug
>>> > (since I don't
>>> > > remember how his
cluster code
works).
>>> > >
>>> > > 4. The
significance doesn't
depend
>>> on the cluster
>>> > size unless you do
>>> > > multiple comparison
corrections (and
>>> even then only
>>> > if you do them a
>>> > > certain way)
>>> > >
>>> > > cheers
>>> > > Bruce
>>> > >
>>> > >
>>> > > On Thu, 23 Jul
2015, A-reum Min
wrote:
>>> > >
>>> > > HELLO developer
>>> > > I have some
question to you..
>>> > >
>>> > > 1. Every
patient is given to the
>>> same number
>>> > of vertex?
>>> > >
>>> > > 2. When i use a
Qdec, How can I
get the
>>> > subject result data?
>>> > >
>>> > > 3. Could i get
the significant
vertex’s
>>> > number, extent of the
>>> > > significant area
and gray matter
volume?
>>> > >
>>> > > 4. Is it
significant blue color
>>> which how
>>> > many connected
>>> > > vertex?
>>> > >
>>> > >
>>> > > 2015-05-29 2:03
GMT+09:00 A-reum Min
>>> > <naniy...@gmail.com
>>> <mailto:naniy...@gmail.com>
<mailto:naniy...@gmail.com
>>> <mailto:naniy...@gmail.com>>
>>> > >
<mailto:naniy...@gmail.com
>>> <mailto:naniy...@gmail.com>
>>> >
<mailto:naniy...@gmail.com
<mailto:naniy...@gmail.com>>>>:
>>> > > hello developer~
>>> > > reconstruction is
well done, so i'm
>>> doing on
>>> > 'qdec' step..
>>> > > Actually, i don't
know how to treat
the
>>> Design
>>> > menu exactly..
>>> > >
>>> >
>>>
--------------------------------------------------------------------------
-
>>> > > Discrete(fixed
factors) : diagnosis
>>> > > continuous
(covariate) : age ,
>>> > Left-Lateral-Ventricle
>>> > >
>>> >
>>>
--------------------------------------------------------------------------
-
>>> > > which one click
before analyze?
>>> > >
>>> > > age range is
12years~24years/
>>> > > all subjects
are adolescent.
>>> > > and no
outlier in age range..
>>> so.. age
>>> > (continuous factor)
does not
>>> > > nasessart?
>>> > >
>>> > >
>>> > > 2015-05-29 1:19
GMT+09:00 A-reum Min
>>> > <naniy...@gmail.com
>>> <mailto:naniy...@gmail.com>
<mailto:naniy...@gmail.com
>>> <mailto:naniy...@gmail.com>>
>>> > >
<mailto:naniy...@gmail.com
>>> <mailto:naniy...@gmail.com>
>>> >
<mailto:naniy...@gmail.com
<mailto:naniy...@gmail.com>>>>:
>>> > > hello developer~
>>> > > reconstruction is
well done, so i'm
>>> doing on
>>> > 'qdec' step..
>>> > > Actually, i don't
know how to treat
the
>>> Design
>>> > menu exactly..
>>> > >
>>> >
>>>
--------------------------------------------------------------------------
-
>>> > > Discrete(fixed
factors) : diagnosis
>>> > > continuous
(covariate) : age ,
>>> > Left-Lateral-Ventricle
>>> > >
>>> >
>>>
--------------------------------------------------------------------------
-
>>> > > which one click
before analyze?
>>> > >
>>> > >
>>> > >
>>> > > 2015-04-05 21:41
GMT+09:00 Bruce
Fischl
>>> > >
<fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>
>>> >
<mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>>
>>> >
<mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>
>>> >
<mailto:fis...@nmr.mgh.harvard.edu
>>>
<mailto:fis...@nmr.mgh.harvard.edu>>>>:
>>> > > I'm glad it worked
out
>>> > > Bruce
>>> > > On Sun, 5 Apr
2015, A-reum Min
wrote:
>>> > >
>>> > > Hello Bruce~
>>> > > You're
right.. my PISA dicom
file
>>> > header
>>> > > is too short
>>> > > so,
freesurfer didn't read
it.
>>> > >
>>> > > Therefore I
use another
subjects
>>> dicom
>>> > > file and
then freesurfer read
it!
>>> > >
>>> > > thank you
for u r adavice to
me.
>>> > >
>>> > > I really
appreciate u
>>> > >
>>> > > 2015-04-05
7:08 GMT+09:00
Bruce
>>> Fischl
>>> > >
<fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>
>>> >
<mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>>
>>> > >
<mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>
>>> >
<mailto:fis...@nmr.mgh.harvard.edu
>>>
<mailto:fis...@nmr.mgh.harvard.edu>>>>:
>>> > > Hi A-reum
>>> > >
>>> > > the
problem is that
newer
>>> > versions
>>> > > of scanner
software
compress
>>> > > dicoms and the
version of FS you
>>> > > have
doesn't know how to
read
>>> > > it.
So you need to
>>> decompress
>>> > them
>>> > > before
passing them to
>>> > > recon-all
>>> > >
>>> > > cheers
>>> > > Bruce
>>> > > On
Sun, 5 Apr 2015,
>>> A-reum Min
>>> > > wrote:
>>> > >
>>> > > Hello developer~
>>> > >
>>> > > Can you summarize
what the
>>> > > problem
is?
>>> > > ==>
>>> > > my problem is
recon-all -i
>>> > > didn't
working...
>>> > > so, if i type the
recon-all
>>> > > -i~then
show up theses
>>> > >
>>> > >
>>> > >
>>> >
>>>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>> > > ERROR: 32512, see
>>> > >
>>> > >
>>>
/tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out
>>> > > for
>>> > > more details
>>> > > Linux
localhost.localdomain
>>> > >
2.6.32-504.el6.x86_64 #1
>>> > > SMP Wed Oct 15
04:27:16
>>> > > UTC 2014 x86_64
x86_64
>>> > > x86_64
GNU/Linux
>>> > >
>>> > > dcmdjpeg.fs: error
while
>>> > > loading
shared libraries:
>>> > > libijg8.so.3.6:
cannot
>>> > > open shared object
file: No
>>> > > such file
or directory
>>> > >
>>> > >
>>> > >
>>> >
>>>
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>> > >
>>> > > then, i click the
>>> > >
>>> > >
>>>
root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out,
>>> > > show
>>> > > up
>>> > > these
>>> > > dcmdjpeg.fs: error
while
>>> > > loading
shared libraries:
>>> > > libijg8.so.3.6:
cannot
>>> > > open shared object
file: No
>>> > > such file
or directory
>>> > >
>>> > > Are you trying to
read
>>> > > compressed
dicom?
>>> > > ==>
>>> > > Am i trying to
read
>>> > > compressed
dicom?
>>> > > I send my
10071579.dicom(i
>>> > > use this)
to you,
>>> > > using -i, convert
the dicom
>>> > > file to
mgh file. i just
>>> > > know that dicom
file
>>> > > convert to mgz
format using
>>> > > -i /my
data path
>>> > > Is it right..??
>>> > >
>>> > >
>>> > > If so, Can you try
running
>>> > > dcmdjpeg
on it to create
>>> > > a new
(uncompressed)
>>> > > series and give
that to
>>> > > recon-all?
>>> > > ==> (actually, i
didn't
>>> > > understand
your sentence
>>> > > means perfectly..)
>>> > > zeke
>>> > >
>>> >
>>>
tomeaurl(ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binarie
s/c
>>> > >
>>> > > en
>>> > > t
>>> > >
os6_x86_64/dcmdjpeg.fs)
>>> > > and then, replace my
>>> > > existing
>>> > >
>>> > >
$FREESURFER_HOME/bin/dcmdjpeg.fs
file.
>>> > > Also, make sure it
is set to
>>> > > executable
by typing
>>> > > the following in a
>>> > > terminal window:
>>> > > $> chmod a+x
>>> > >
$FREESURFER_HOME/bin/dcmdjpeg.fs
>>> > >
>>> > >
>>> > > 2015-04-05 2:30
GMT+09:00
>>> > > Bruce
Fischl
>>> > >
>>> > >
<fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>
>>> >
<mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>>
>>> > >
<mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>
>>> >
<mailto:fis...@nmr.mgh.harvard.edu
>>>
<mailto:fis...@nmr.mgh.harvard.edu>>>>:
>>> > > Hi A-reum
>>> > >
>>> > > sorry, I'm coming
into
>>> > > this late.
Can you
>>> > > summarize what the
>>> > > problem is? Are you
>>> > > trying to
read compressed
>>> > > dicom? If so, can
>>> > > you try running
>>> > > dcmdjpeg
on it to create a
new
>>> > > (uncompressed)
>>> > > series and give
that
>>> > > to
recon-all?
>>> > >
>>> > > cheers
>>> > > Bruec
>>> > >
>>> > >
>>> > >
>>> > > On Sat, 4
Apr 2015,
>>> > > A-reum Min
wrote:
>>> > >
>>> > > Hello
>>> > > developers..
>>> > >
>>> > > i type the
>>> > > recon-all
-i~then show up
>>> > > theses
>>> > >
>>> > >
>>> > >
>>> > >
>>> >
>>>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>> > > ERROR: 32512,
>>> > > see
>>> > >
>>> > >
>>> > >
>>>
/tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out
>>> > > for
>>> > > more details
>>> > > Linux
>>> > >
localhost.localdomain
>>> > >
2.6.32-504.el6.x86_64 #1
>>> > > SMP Wed Oct 15
>>> > > 04:27:16
>>> > > UTC 2014 x86_64
>>> > > x86_64
x86_64 GNU/Linux
>>> > >
>>> > > dcmdjpeg.fs:
>>> > > error
while loading shared
>>> > > libraries:
>>> > > libijg8.so.3.6:
>>> > > cannot
>>> > > open shared
>>> > > object
file: No such file
or
>>> > > directory
>>> > >
>>> > >
>>> > >
>>> > >
>>> >
>>>
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>> > >
>>> > > error is occured
>>> > > (a little
differntly..)
>>> > > then, i click
>>> > > the
>>> > >
>>> > >
>>> > >
>>>
root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out,
>>> > > show
>>> > > up
>>> > > these
>>> > >
>>> > > dcmdjpeg.fs:
>>> > > error
while loading shared
>>> > > libraries:
>>> > > libijg8.so.3.6:
>>> > > cannot
>>> > > open shared
>>> > > object
file: No such file
or
>>> > > directory
>>> > >
>>> > > i'm so sorry..to
>>> > > bother
you..
>>> > >
>>> > >
>>> > >
>>> > > 2015-04-04 9:21
>>> > > GMT+09:00
A-reum Min
>>> > >
>>> > >
<naniy...@gmail.com
>>> <mailto:naniy...@gmail.com>
>>> >
<mailto:naniy...@gmail.com
>>> <mailto:naniy...@gmail.com>>
<mailto:naniy...@gmail.com
>>> <mailto:naniy...@gmail.com>
>>> >
<mailto:naniy...@gmail.com
>>> <mailto:naniy...@gmail.com>>>>:
>>> > > hello
>>> > >
>>> > > i type the
>>> > > recon-all
-i~
>>> > > then show up
>>> > > theses
>>> > >
>>> >
>>>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
>>> > >
>>> > >
>>> > >
>>> > > +++++++
>>> > >
>>> > > ERROR: 32256,
>>> > > see
>>> > >
>>> > >
>>> > >
>>>
/tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out
>>> > > for more details
>>> > > Linux
>>> > >
localhost.localdomain
>>> > >
2.6.32-504.el6.x86_64 #1
>>> > > SMP Wed Oct 15
>>> > > 04:27:16 UTC
>>> > > 2014
x86_64 x86_64 x86_64
>>> > > GNU/Linux
>>> > >
>>> >
>>>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
>>> > >
>>> > >
>>> > >
>>> > > +++++++
>>> > > the error is
>>> > > occured (a
little
>>> > > differntly..)
>>> > > then, i click
>>> > > the
>>> > >
>>> > >
>>> > >
>>>
/tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out,
>>> > > show iuo these
>>> > >
>>> > > sh:
>>> > >
>>> > >
/usr/local/freesurfer/bin/dcmdjpeg.fs:
>>> > >
>>> > > /lib/ld-linux.so.2:
bad ELF
>>> > > interpreter: No
>>> > > such file
or directory
>>> > >
>>> > > plz help me
>>> > > 2015-04-04 4:12
>>> > > GMT+09:00
>>> > >
>>> > >
<zkauf...@nmr.mgh.harvard.edu
>>>
<mailto:zkauf...@nmr.mgh.harvard.edu>
>>> >
<mailto:zkauf...@nmr.mgh.harvard.edu
>>>
<mailto:zkauf...@nmr.mgh.harvard.edu>>
>>> > >
<mailto:zkauf...@nmr.mgh.harvard.edu
>>>
<mailto:zkauf...@nmr.mgh.harvard.edu>
>>> >
<mailto:zkauf...@nmr.mgh.harvard.edu
>>>
<mailto:zkauf...@nmr.mgh.harvard.edu>>>>:
>>> > > A-reum,
>>> > >
>>> > > Please
>>> > > download
the following
>>> > > file:
>>> > >
>>> > >
>>> >
>>>
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6
_
>>> > >
>>> > >
>>> > >
>>> > >
>>> > > x86_64/dcmdjpeg.fs
>>> > >
>>> > > And
>>> > > replace
your existing
>>> > >
>>> > >
$FREESURFER_HOME/bin/dcmdjpeg.fs
>>> > > file with
>>> > > the
>>> > > one from
>>> > > the link
above. Also,
>>> > > make sure it is
>>> > > set to
>>> > > executable
>>> > > by typing
>>> > > the
>>> > > following
in a terminal
>>> > > window:
>>> > >
>>> > > $> chmod
>>> > > a+x
>>> > >
>>> > >
$FREESURFER_HOME/bin/dcmdjpeg.fs
>>> > >
>>> > > And then
>>> > > try again.
>>> > >
>>> > > -Zeke
>>> > >
>>> > >
>>> > > > Hi
>>> > > doug...
recon-all dosen't
>>> > > working..
>>> > > >
>>> > > > If i
>>> > > type the
recon-all -i~
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