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 me2015-11-10 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>>:
> <mailto:naniyaah@gmail.com>>:>
> 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/001-iscale.txt
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.txt
> --subsample 200 --lta
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta
>
>
> $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10
> 19:59:06 mreuter Exp $
>
> --mov: Using
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
> as
> movable/source volume.
> --mov: Using
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> as
> movable/source volume.
> Total: 2 input volumes
> --average: Using method 1 for template computation.
> --template: Using
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz
> as
> template output volume.
> --satit: Will estimate SAT iteratively!
> --inittp: Using TP 1 as target for initialization
> --fixtp: Will map everything to init TP!
> --noit: Will output only first template (no iterations)!
> --iscale: Enableing intensity scaling!
> --iscaleout: Will perform intensity scaling and output results
> --subsample: Will subsample if size is larger than 200 on
> all axes!
> --lta: Will output LTA transforms
> reading source
> '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'...
> converting source
> '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'
> to
> bspline ...
> MRItoBSpline degree 3
> reading source
> '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'...
> converting source
> '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'
> to
> bspline ...
> MRItoBSpline degree 3
>
> MultiRegistration::initializing Xforms (init 1 , maxres 0
> , iterate 5 ,
> epsit 0.01 ) :
>
> [init] ========================= TP 2 to TP 1
> ==============================
> Register TP 2 (
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> )
> to TP 1 (
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
> )
>
> -- Original : (0.4688, 0.4688, 0.800001) mm size
> and (512, 512, 244)
> voxels.
> -- Resampled: (0.4688, 0.4688, 0.4688) mm size and
> (512, 512, 417)
> voxels.
> -- Reslicing using cubic bspline
> MRItoBSpline degree 3
> -- Original : (0.4688, 0.4688, 0.800001) mm size
> and (512, 512, 244)
> voxels.
> -- Resampled: (0.4688, 0.4688, 0.4688) mm size and
> (512, 512, 417)
> voxels.
> -- Reslicing using cubic bspline
> MRItoBSpline degree 3
>
> - Max Resolution used: 3
> -- gpS ( 64 , 64 , 52 )
> -- gpT ( 64 , 64 , 52 )
> - running loop to estimate saturation parameter:
> Sigma too small: 0 (identical images?)
> Sigma too small: 0 (identical images?)
> Sigma too small: 0 (identical images?)
> Sigma too small: 0 (identical images?)
> Sigma too small: 0 (identical images?)
> Sigma too small: 0 (identical images?)
> Sigma too small: 0 (identical images?)
> Sigma too small: 0 (identical images?)
> Sigma too small: 0 (identical images?)
> Sigma too small: 0 (identical images?)
> Killed
> Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP
> Wed Oct 15 04:27:16
> UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s sub002 exited with ERRORS at Thu Nov 5
> 02:37:57 PST 2015
>
> For more details, see the log file
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
> 2015-10-19 11:05 GMT+09:00 A-reum Min <naniyaah@gmail.com
> <mailto:fischl@nmr.mgh.harvard.edu>>:> 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
> 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>>:
> <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
> 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> <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:naniyaah@gmail.com> <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> <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:Freesurfer@nmr.mgh.harvard.edu>> <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 <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 <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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>
>
> The information in this e-mail is intended only for the person
> to whom it is
> addressed. If you believe this e-mail was sent to you in error
> and the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
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> but does not contain patient information, please contact the
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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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