Hi A-reumdid you talk to the Wash U group? If you have nifti files they can be processed using recon-all (i.e. recon-all -i <full path to nifti file> -s <subject id> -sd <directory to contain all subjects> -all)
cheers BruceOn Tue, 29 Dec 2015, A-reum Min wrote:
hello experts!my name is areum.
i have some question to you.i have never seen before these NIFTI
format(fig.1.png)
I want to see these data subjects's cortical thickness using qdec.
how can i to do? plz answer me
2015-12-25 2:16 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:
Hi A-reum
you should probably ask the Wash U HCP group. I'll cc Matt
Glasser who might be able to answer your question
cheers
Bruce
On Thu, 24 Dec 2015, A-reum Min wrote:
hello experts!my name is areum.
i have some question to you.
a few days ago i was down load HCP(human connectom
project) data.
but.. how can i use these HCP format.
i have never seen before these format(fig.1.png)
I want to see HCP data subjects's cortical thickness
using qdec.
how can i to do?
plz answer me
2015-11-10 7:49 GMT+09:00 A-reum Min
<naniy...@gmail.com>:
Hello experts!
I have some question to you..
I don't need to show up so small blue regions(fig.1
blue region)
How can i control these?
2015-11-10 7:41 GMT+09:00 Douglas N Greve
<gr...@nmr.mgh.harvard.edu>:
Hi, please create a new thread since this is a
new topic.
Also, I don't
understand your question so please elaborate.
On 11/09/2015 05:34 AM, A-reum Min wrote:
> Hello experts!
>
> i have some question to you..
>
> How can i control the cluster size?
>
> My cluster threshold is 1.
>
> then, too many blue regions (as shown
fig.1).
>
> so, i want to control cluster threshold 1-->
cluster
threshold 5.
>
> 2015-11-08 20:44 GMT+09:00 A-reum Min
<naniy...@gmail.com
> <mailto:naniy...@gmail.com>>:
>
> Hello bruce!
>
> I solve the problem for your answer.
>
> And.. i have some question to you..
>
> How can i control the cluster size?
>
> My cluster threshold is 1.
>
> then, too many blue regions (as shown
fig.1).
>
> so, i want to control cluster threshold
1--> cluster
threshold 5.
>
> How can i to do?
>
>
>
>
>
> 2015-11-05 22:22 GMT+09:00 Bruce Fischl
> <fis...@nmr.mgh.harvard.edu
<mailto:fis...@nmr.mgh.harvard.edu>>:
>
> are
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm
> and
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm
> images from *different* series or
from the
*same* series? If
> they are in the same series than
that explains
what is
> happening. You should only give
recon-all a
single file from
> any one acquisition - it will figure
out the
rest of the files
> that are part of it.
>
> cheers
> Bruce
>
>
> On Thu, 5 Nov 2015, A-reum Min
wrote:
>
> 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/0
0
1-iscale.txt
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.t
x
t
> --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
> <mailto: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
> <mailto: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
> <mailto: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
> <mailto: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>
> >
<mailto: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
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
