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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