Dear experts,
I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file”
Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated.
Thanks,
Osorio
-----Original Message----- From: Meirelles, Osorio (NIH/NIA/IRP) [E] Sent: Thursday, December 24, 2015 12:23 PM To: Freesurfer support list Cc: Matthew Glasser Subject: RE: [Freesurfer] hello freesurfer developer~
Dear experts,
I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file”
Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated.
Thanks,
Osorio
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 24, 2015 12:16 PM To: Freesurfer support list Cc: Matthew Glasser Subject: Re: [Freesurfer] hello freesurfer developer~
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 naniyaah@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 greve@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 <naniyaah@gmail.com > <mailto:naniyaah@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 > <fischl@nmr.mgh.harvard.edu <mailto:fischl@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/00 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.tx 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 <naniyaah@gmail.commailto:naniyaah@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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@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
<greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>> <naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com
>>> > <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> <naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com
>>> >
<mailto:naniyaah@gmail.com
mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>>>: >>> > >>> > Hello bruce >>> > >>> > I solve this problem(12.png) >>> > >>> > Thank you >>> > >>> > 2015-07-27 13:03
GMT+09:00
dgw >>> <dgwakeman@gmail.com mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com> >>> > <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com >>> <mailto:dgwakeman@gmail.com mailto:dgwakeman@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 >>> > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@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 >>> > <naniyaah@gmail.com mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> > <naniyaah@gmail.com mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@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 >>> > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>
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Hi Osorio,
Are you sure the file completely downloaded without errors? You can confirm this by running:
sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
The output of this command should match the result on this webpage: http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/sha1sum.txt
If your file is uncorrupted, try running this command to unzip it:
tar xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
Best, Lee
On Mon, 28 Dec 2015, Meirelles, Osorio (NIH/NIA/IRP) [E] wrote:
Dear experts,
I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file”
Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated.
Thanks,
Osorio
-----Original Message----- From: Meirelles, Osorio (NIH/NIA/IRP) [E] Sent: Thursday, December 24, 2015 12:23 PM To: Freesurfer support list Cc: Matthew Glasser Subject: RE: [Freesurfer] hello freesurfer developer~
Dear experts,
I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file”
Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated.
Thanks,
Osorio
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 24, 2015 12:16 PM To: Freesurfer support list Cc: Matthew Glasser Subject: Re: [Freesurfer] hello freesurfer developer~
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 naniyaah@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 greve@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 <naniyaah@gmail.com > <mailto:naniyaah@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 > <fischl@nmr.mgh.harvard.edu <mailto:fischl@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/00 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.tx 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 <naniyaah@gmail.commailto:naniyaah@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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@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
<greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>> <naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com
>>> > <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> <naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com
>>> >
<mailto:naniyaah@gmail.com
mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>>>: >>> > >>> > Hello bruce >>> > >>> > I solve this problem(12.png) >>> > >>> > Thank you >>> > >>> > 2015-07-27 13:03
GMT+09:00
dgw >>> <dgwakeman@gmail.com mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com> >>> > <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com >>> <mailto:dgwakeman@gmail.com mailto:dgwakeman@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 >>> > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@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 >>> > <naniyaah@gmail.com mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> > <naniyaah@gmail.com mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@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 >>> > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>
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Hi Lee,
I guess it worked. It looks like several hundreds of files were unzipped., however, in the end, there was still the following message:
gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now
At this stage I do not know if this is a minor error or if there were many more files to be unzipped that were not since the process was interrupted.
What would you recommend I do next?
Thank you,
Osorio
-----Original Message----- From: Lee Tirrell [mailto:ltirrell@nmr.mgh.harvard.edu] Sent: Monday, December 28, 2015 1:46 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cannot open FreeSurfer application zipped file
Hi Osorio,
Are you sure the file completely downloaded without errors? You can confirm this by running:
sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
The output of this command should match the result on this webpage: http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/sha1sum.txt
If your file is uncorrupted, try running this command to unzip it:
tar xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
Best, Lee
On Mon, 28 Dec 2015, Meirelles, Osorio (NIH/NIA/IRP) [E] wrote:
Dear experts,
I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file”
Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated.
Thanks,
Osorio
-----Original Message----- From: Meirelles, Osorio (NIH/NIA/IRP) [E] Sent: Thursday, December 24, 2015 12:23 PM To: Freesurfer support list Cc: Matthew Glasser Subject: RE: [Freesurfer] hello freesurfer developer~
Dear experts,
I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file”
Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated.
Thanks,
Osorio
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 24, 2015 12:16 PM To: Freesurfer support list Cc: Matthew Glasser Subject: Re: [Freesurfer] hello freesurfer developer~
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 naniyaah@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 greve@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 <naniyaah@gmail.com > <mailto:naniyaah@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 > <fischl@nmr.mgh.harvard.edu <mailto:fischl@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/00 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.tx 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 <naniyaah@gmail.commailto:naniyaah@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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@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
<greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>> <naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com
>>> > <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> <naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com
>>> >
<mailto:naniyaah@gmail.com
mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>>>: >>> > >>> > Hello bruce >>> > >>> > I solve this problem(12.png) >>> > >>> > Thank you >>> > >>> > 2015-07-27 13:03
GMT+09:00
dgw >>> <dgwakeman@gmail.com mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com> >>> > <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com >>> <mailto:dgwakeman@gmail.com mailto:dgwakeman@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 >>> > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@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 >>> > <naniyaah@gmail.com mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> > <naniyaah@gmail.com mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@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 >>> > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Did you confirm that the sha1sum of your tar.gz file matches the one on the website?
On Mon, 28 Dec 2015, Meirelles, Osorio (NIH/NIA/IRP) [E] wrote:
Hi Lee,
I guess it worked. It looks like several hundreds of files were unzipped., however, in the end, there was still the following message:
gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now
At this stage I do not know if this is a minor error or if there were many more files to be unzipped that were not since the process was interrupted.
What would you recommend I do next?
Thank you,
Osorio
-----Original Message----- From: Lee Tirrell [mailto:ltirrell@nmr.mgh.harvard.edu] Sent: Monday, December 28, 2015 1:46 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cannot open FreeSurfer application zipped file
Hi Osorio,
Are you sure the file completely downloaded without errors? You can confirm this by running:
sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
The output of this command should match the result on this webpage: http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/sha1sum.txt
If your file is uncorrupted, try running this command to unzip it:
tar xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
Best, Lee
On Mon, 28 Dec 2015, Meirelles, Osorio (NIH/NIA/IRP) [E] wrote:
Dear experts,
I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file”
Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated.
Thanks,
Osorio
-----Original Message----- From: Meirelles, Osorio (NIH/NIA/IRP) [E] Sent: Thursday, December 24, 2015 12:23 PM To: Freesurfer support list Cc: Matthew Glasser Subject: RE: [Freesurfer] hello freesurfer developer~
Dear experts,
I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file”
Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated.
Thanks,
Osorio
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 24, 2015 12:16 PM To: Freesurfer support list Cc: Matthew Glasser Subject: Re: [Freesurfer] hello freesurfer developer~
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 naniyaah@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 greve@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 <naniyaah@gmail.com > <mailto:naniyaah@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 > <fischl@nmr.mgh.harvard.edu <mailto:fischl@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/00 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.tx 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 <naniyaah@gmail.commailto:naniyaah@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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@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
<greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>> <naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com
>>> > <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> <naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com
>>> >
<mailto:naniyaah@gmail.com
mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>>>: >>> > >>> > Hello bruce >>> > >>> > I solve this problem(12.png) >>> > >>> > Thank you >>> > >>> > 2015-07-27 13:03
GMT+09:00
dgw >>> <dgwakeman@gmail.com mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com> >>> > <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com >>> <mailto:dgwakeman@gmail.com mailto:dgwakeman@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 >>> > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@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 >>> > <naniyaah@gmail.com mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> > <naniyaah@gmail.com mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@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 >>> > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>
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to whom it is addressed. If you believe this e-mail was sent to you
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Hi Lee,
I ran the command " sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz" and I got the result 7c03e796e9b81ee69aaa60079c4094f20b945c08 where it should have been 0c8d784e28a435bd5ea45be6a461990894cfc5b7 , according to the webpage: http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/sha1sum.txt
So does this mean that I have a Freesurfer corrupted installation file? What would you recommend? Can you suggest me a link to download a more updated version?
Thanks,
Osorio
-----Original Message----- From: Meirelles, Osorio (NIH/NIA/IRP) [E] Sent: Monday, December 28, 2015 2:07 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cannot open FreeSurfer application zipped file
Hi Lee,
I guess it worked. It looks like several hundreds of files were unzipped., however, in the end, there was still the following message:
gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now
At this stage I do not know if this is a minor error or if there were many more files to be unzipped that were not since the process was interrupted.
What would you recommend I do next?
Thank you,
Osorio
-----Original Message----- From: Lee Tirrell [mailto:ltirrell@nmr.mgh.harvard.edu] Sent: Monday, December 28, 2015 1:46 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cannot open FreeSurfer application zipped file
Hi Osorio,
Are you sure the file completely downloaded without errors? You can confirm this by running:
sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
The output of this command should match the result on this webpage: http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/sha1sum.txt
If your file is uncorrupted, try running this command to unzip it:
tar xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
Best, Lee
On Mon, 28 Dec 2015, Meirelles, Osorio (NIH/NIA/IRP) [E] wrote:
Dear experts,
I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file”
Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated.
Thanks,
Osorio
-----Original Message----- From: Meirelles, Osorio (NIH/NIA/IRP) [E] Sent: Thursday, December 24, 2015 12:23 PM To: Freesurfer support list Cc: Matthew Glasser Subject: RE: [Freesurfer] hello freesurfer developer~
Dear experts,
I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file”
Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated.
Thanks,
Osorio
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 24, 2015 12:16 PM To: Freesurfer support list Cc: Matthew Glasser Subject: Re: [Freesurfer] hello freesurfer developer~
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 naniyaah@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 greve@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 <naniyaah@gmail.com > <mailto:naniyaah@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 > <fischl@nmr.mgh.harvard.edu <mailto:fischl@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/00 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.tx 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 <naniyaah@gmail.commailto:naniyaah@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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@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
<greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>> <naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com
>>> > <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> <naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com
>>> >
<mailto:naniyaah@gmail.com
mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>>>: >>> > >>> > Hello bruce >>> > >>> > I solve this problem(12.png) >>> > >>> > Thank you >>> > >>> > 2015-07-27 13:03
GMT+09:00
dgw >>> <dgwakeman@gmail.com mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com> >>> > <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com >>> <mailto:dgwakeman@gmail.com mailto:dgwakeman@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 >>> > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@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 >>> > <naniyaah@gmail.com mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> > <naniyaah@gmail.com mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@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 >>> > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>
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Hi Osorio,
I looked at that webpage, and it seems you have the correct result. The sha1sum of freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz is 7c03e796e9b81ee69aaa60079c4094f20b945c08, so your file should be fine.
Best, Lee
On Wed, 27 Jan 2016, Meirelles, Osorio (NIH/NIA/IRP) [E] wrote:
Hi Lee,
I ran the command " sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz" and I got the result 7c03e796e9b81ee69aaa60079c4094f20b945c08 where it should have been 0c8d784e28a435bd5ea45be6a461990894cfc5b7 , according to the webpage: http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/sha1sum.txt
So does this mean that I have a Freesurfer corrupted installation file? What would you recommend? Can you suggest me a link to download a more updated version?
Thanks,
Osorio
-----Original Message----- From: Meirelles, Osorio (NIH/NIA/IRP) [E] Sent: Monday, December 28, 2015 2:07 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cannot open FreeSurfer application zipped file
Hi Lee,
I guess it worked. It looks like several hundreds of files were unzipped., however, in the end, there was still the following message:
gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now
At this stage I do not know if this is a minor error or if there were many more files to be unzipped that were not since the process was interrupted.
What would you recommend I do next?
Thank you,
Osorio
-----Original Message----- From: Lee Tirrell [mailto:ltirrell@nmr.mgh.harvard.edu] Sent: Monday, December 28, 2015 1:46 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cannot open FreeSurfer application zipped file
Hi Osorio,
Are you sure the file completely downloaded without errors? You can confirm this by running:
sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
The output of this command should match the result on this webpage: http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/sha1sum.txt
If your file is uncorrupted, try running this command to unzip it:
tar xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
Best, Lee
On Mon, 28 Dec 2015, Meirelles, Osorio (NIH/NIA/IRP) [E] wrote:
Dear experts,
I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file”
Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated.
Thanks,
Osorio
-----Original Message----- From: Meirelles, Osorio (NIH/NIA/IRP) [E] Sent: Thursday, December 24, 2015 12:23 PM To: Freesurfer support list Cc: Matthew Glasser Subject: RE: [Freesurfer] hello freesurfer developer~
Dear experts,
I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file”
Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated.
Thanks,
Osorio
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 24, 2015 12:16 PM To: Freesurfer support list Cc: Matthew Glasser Subject: Re: [Freesurfer] hello freesurfer developer~
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 naniyaah@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 greve@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 <naniyaah@gmail.com > <mailto:naniyaah@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 > <fischl@nmr.mgh.harvard.edu <mailto:fischl@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/00 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.tx 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 <naniyaah@gmail.commailto:naniyaah@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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@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
<greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>> <naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com
>>> > <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> <naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com
>>> >
<mailto:naniyaah@gmail.com
mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>>>: >>> > >>> > Hello bruce >>> > >>> > I solve this problem(12.png) >>> > >>> > Thank you >>> > >>> > 2015-07-27 13:03
GMT+09:00
dgw >>> <dgwakeman@gmail.com mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com> >>> > <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com >>> <mailto:dgwakeman@gmail.com mailto:dgwakeman@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 >>> > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@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 >>> > <naniyaah@gmail.com mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> > <naniyaah@gmail.com mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@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 >>> > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Hi Lee,
Sorry, my mistake, I actually got 0c8d784e28a435bd5ea45be6a461990894cfc5b7 when it should be 7c03e796e9b81ee69aaa60079c4094f20b945c08.
I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then after a lot of files were unzipped I got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file”
Thanks,
Osorio
-----Original Message----- From: Lee Tirrell [mailto:ltirrell@nmr.mgh.harvard.edu] Sent: Wednesday, January 27, 2016 1:14 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cannot open FreeSurfer application zipped file
Hi Osorio,
I looked at that webpage, and it seems you have the correct result. The sha1sum of freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz is 7c03e796e9b81ee69aaa60079c4094f20b945c08, so your file should be fine.
Best, Lee
On Wed, 27 Jan 2016, Meirelles, Osorio (NIH/NIA/IRP) [E] wrote:
Hi Lee,
I ran the command " sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz" and I got the result 7c03e796e9b81ee69aaa60079c4094f20b945c08 where it should have been 0c8d784e28a435bd5ea45be6a461990894cfc5b7 , according to the webpage: http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/sha1sum.txt
So does this mean that I have a Freesurfer corrupted installation file? What would you recommend? Can you suggest me a link to download a more updated version?
Thanks,
Osorio
-----Original Message----- From: Meirelles, Osorio (NIH/NIA/IRP) [E] Sent: Monday, December 28, 2015 2:07 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cannot open FreeSurfer application zipped file
Hi Lee,
I guess it worked. It looks like several hundreds of files were unzipped., however, in the end, there was still the following message:
gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now
At this stage I do not know if this is a minor error or if there were many more files to be unzipped that were not since the process was interrupted.
What would you recommend I do next?
Thank you,
Osorio
-----Original Message----- From: Lee Tirrell [mailto:ltirrell@nmr.mgh.harvard.edu] Sent: Monday, December 28, 2015 1:46 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cannot open FreeSurfer application zipped file
Hi Osorio,
Are you sure the file completely downloaded without errors? You can confirm this by running:
sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
The output of this command should match the result on this webpage: http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/sha1sum.txt
If your file is uncorrupted, try running this command to unzip it:
tar xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
Best, Lee
On Mon, 28 Dec 2015, Meirelles, Osorio (NIH/NIA/IRP) [E] wrote:
Dear experts,
I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file”
Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated.
Thanks,
Osorio
-----Original Message----- From: Meirelles, Osorio (NIH/NIA/IRP) [E] Sent: Thursday, December 24, 2015 12:23 PM To: Freesurfer support list Cc: Matthew Glasser Subject: RE: [Freesurfer] hello freesurfer developer~
Dear experts,
I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file”
Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated.
Thanks,
Osorio
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 24, 2015 12:16 PM To: Freesurfer support list Cc: Matthew Glasser Subject: Re: [Freesurfer] hello freesurfer developer~
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 naniyaah@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 greve@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 <naniyaah@gmail.com > <mailto:naniyaah@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 > <fischl@nmr.mgh.harvard.edu <mailto:fischl@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/00 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.tx 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 <naniyaah@gmail.commailto:naniyaah@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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@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
<greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>> <naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com
>>> > <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> <naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com
>>> >
<mailto:naniyaah@gmail.com
mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>>>: >>> > >>> > Hello bruce >>> > >>> > I solve this problem(12.png) >>> > >>> > Thank you >>> > >>> > 2015-07-27 13:03
GMT+09:00
dgw >>> <dgwakeman@gmail.com mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com> >>> > <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com >>> <mailto:dgwakeman@gmail.com mailto:dgwakeman@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 >>> > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@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 >>> > <naniyaah@gmail.com mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> > <naniyaah@gmail.com mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@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 >>> > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>
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It seems to be something wrong with the download. Either you ran of disk space, the download never completed, or you started to untar it before the download completed. There have been problems in the past if you used the Safari web browser to download it, so try Firefox or Chrome if you used Safari.
Also, you can download it directly from the command line (all in one line):
curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
Best, Lee
On Wed, 27 Jan 2016, Meirelles, Osorio (NIH/NIA/IRP) [E] wrote:
Hi Lee,
Sorry, my mistake, I actually got 0c8d784e28a435bd5ea45be6a461990894cfc5b7 when it should be 7c03e796e9b81ee69aaa60079c4094f20b945c08.
I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then after a lot of files were unzipped I got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file”
Thanks,
Osorio
-----Original Message----- From: Lee Tirrell [mailto:ltirrell@nmr.mgh.harvard.edu] Sent: Wednesday, January 27, 2016 1:14 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cannot open FreeSurfer application zipped file
Hi Osorio,
I looked at that webpage, and it seems you have the correct result. The sha1sum of freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz is 7c03e796e9b81ee69aaa60079c4094f20b945c08, so your file should be fine.
Best, Lee
On Wed, 27 Jan 2016, Meirelles, Osorio (NIH/NIA/IRP) [E] wrote:
Hi Lee,
I ran the command " sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz" and I got the result 7c03e796e9b81ee69aaa60079c4094f20b945c08 where it should have been 0c8d784e28a435bd5ea45be6a461990894cfc5b7 , according to the webpage: http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/sha1sum.txt
So does this mean that I have a Freesurfer corrupted installation file? What would you recommend? Can you suggest me a link to download a more updated version?
Thanks,
Osorio
-----Original Message----- From: Meirelles, Osorio (NIH/NIA/IRP) [E] Sent: Monday, December 28, 2015 2:07 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cannot open FreeSurfer application zipped file
Hi Lee,
I guess it worked. It looks like several hundreds of files were unzipped., however, in the end, there was still the following message:
gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now
At this stage I do not know if this is a minor error or if there were many more files to be unzipped that were not since the process was interrupted.
What would you recommend I do next?
Thank you,
Osorio
-----Original Message----- From: Lee Tirrell [mailto:ltirrell@nmr.mgh.harvard.edu] Sent: Monday, December 28, 2015 1:46 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cannot open FreeSurfer application zipped file
Hi Osorio,
Are you sure the file completely downloaded without errors? You can confirm this by running:
sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
The output of this command should match the result on this webpage: http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/sha1sum.txt
If your file is uncorrupted, try running this command to unzip it:
tar xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
Best, Lee
On Mon, 28 Dec 2015, Meirelles, Osorio (NIH/NIA/IRP) [E] wrote:
Dear experts,
I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file”
Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated.
Thanks,
Osorio
-----Original Message----- From: Meirelles, Osorio (NIH/NIA/IRP) [E] Sent: Thursday, December 24, 2015 12:23 PM To: Freesurfer support list Cc: Matthew Glasser Subject: RE: [Freesurfer] hello freesurfer developer~
Dear experts,
I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file”
Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated.
Thanks,
Osorio
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 24, 2015 12:16 PM To: Freesurfer support list Cc: Matthew Glasser Subject: Re: [Freesurfer] hello freesurfer developer~
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 naniyaah@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 greve@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
<naniyaah@gmail.comHello 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 <fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu>>:are
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcmand
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcmimages from *different* series or from the
*same* series? Ifthey are in the same series than that explains
what ishappening. You should only give recon-all a
single file fromany one acquisition - it will figure out the
rest of the filesthat 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-v5.3.0Current Stamp:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0INFO: 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 SMPWed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002mri_convert
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgzmri_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 mreuterExp $ reading from
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm...Starting DICOMRead2() dcmfile =
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcmdcmdir =
/usr/local/freesurfer/subjects/OSA/0165766_1Ref 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=12.00i_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/sub002mri_convert
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgzmri_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 mreuterExp $ reading from
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm...Starting DICOMRead2() dcmfile =
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcmdcmdir =
/usr/local/freesurfer/subjects/OSA/0165766_1Ref 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=12.00i_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.mgzChecking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs...
#-----------------------------------------------/usr/local/freesurfer/subjects/OSA/0165766_1/sub002mri_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/00
1-iscale.txt/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.tx
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
2012/10/1019:59:06 mreuter Exp $
--mov: Using
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgzas movable/source volume. --mov: Using
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgzas 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.mgzas 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 onall 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 sizeand (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 sizeand (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 SMPWed 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 502:37:57 PST 2015
For more details, see the log file
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.logTo report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting2015-10-19 11:05 GMT+09:00 A-reum Min
<naniyaah@gmail.commailto:naniyaah@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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@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
<greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 >>> <naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com
>>> > <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> <naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com
>>> >
<mailto:naniyaah@gmail.com
mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>>>: >>> > >>> > Hello bruce >>> > >>> > I solve this problem(12.png) >>> > >>> > Thank you >>> > >>> > 2015-07-27 13:03
GMT+09:00
dgw >>> <dgwakeman@gmail.com mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com> >>> > <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com >>> <mailto:dgwakeman@gmail.com mailto:dgwakeman@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 >>> > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@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 >>> > <naniyaah@gmail.com mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> > <naniyaah@gmail.com mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com mailto:naniyaah@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 >>> > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@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 >>> > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>
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Lee Tirrell -
Meirelles, Osorio (NIH/NIA/IRP) [E]