Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate.
On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniy...@gmail.com > <mailto:naniy...@gmail.com>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... > #-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... > #----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > --average 1 --template > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale > > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001-iscale.txt > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.txt > --subsample 200 --lta > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta > > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > as > movable/source volume. > --mov: Using > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source > > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... > converting source > > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source > > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... > converting source > > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > ) > to TP 1 ( > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > > - Max Resolution used: 3 > -- gpS ( 64 , 64 , 52 ) > -- gpT ( 64 , 64 , 52 ) > - running loop to estimate saturation parameter: > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Killed > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s sub002 exited with ERRORS at Thu Nov 5 > 02:37:57 PST 2015 > > For more details, see the log file > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > 2015-10-19 11:05 GMT+09:00 A-reum Min <naniy...@gmail.com > <mailto:naniy...@gmail.com>>: > hello experts. > i have a question to you.. > > i'm doing recon-all stage, but errors show up like this > > > > > ects/OSA/14/subj014/mri/orig/002.mgz --average 1 --template > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale --iscaleout > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt > --subsample 200 --lta > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta > > / > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter > Exp $ > > --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > as > movable/source volume. > --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source > > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source > > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 > , epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > ) > to TP 1 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, > 244) voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, > 417) voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, > 244) voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, > 417) voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > > - Max Resolution used: 3 > -- gpS ( 64 , 64 , 52 ) > -- gpT ( 64 , 64 , 52 ) > - running loop to estimate saturation parameter: > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Killed > [areum@localhost 14]# > > [areum@localhost 14]# $Id: mri_robust_template.cpp,v 1.37.2.2 > 2012/10/10 19:59:06 mreuter Exp $ > c > Bad : modifier in $ ( ). > [areum@localhost 14]# > [areum@localhost 14]# --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > as > movable/source volume. > --mov:: Too many arguments. > [areum@localhost 14]# --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > as > movable/source volume. > --mov:: Too many arguments. > [areum@localhost 14]# Total: 2 input volumes > Total:: Too many arguments. > b > [areum@localhost 14]# --average: Using method 1 for template > computation. > --average:: Too many arguments. > [areum@localhost 14]# --template: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > as > template output volume. > --template:: Too many arguments. > [areum@localhost 14]# --satit: Will estimate SAT iteratively! > i > --satit:: Too many arguments. > [areum@localhost 14]# --inittp: Using TP 1 as target for > initialization > --inittp:: Too many arguments. > [areum@localhost 14]# --fixtp: Will map everything to init TP! > --fixtp:: Too many arguments. > [areum@localhost 14]# --noit: Will output only first > template (no > iterations)! > Badly placed ()'s. > [areum@localhost 14]# --iscale: Enableing intensity scaling! > --iscale:: Too many arguments. > [areum@localhost 14]# --iscaleout: Will perform intensity > scaling and > output results > --iscaleout:: Too many arguments. > [areum@localhost 14]# --subsample: Will subsample if size > is larger > than 200 on all axes! > --subsample:: Too many arguments. > [areum@localhost 14]# --lta: Will output LTA transforms > --lta:: Too many arguments. > [areum@localhost 14]# reading source > > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > - > reading: Command not found. > [areum@localhost 14]# converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > to > bspline ... > b > converting: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > r > MRItoBSpline: Command not found. > [areum@localhost 14]# reading source > > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... > n > reading: Command not found. > [areum@localhost 14]# converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' > to > bspline ... > > converting: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > p > MRItoBSpline: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# MultiRegistration::initializing > Xforms (init 1 , > maxres 0 , iterate 5 , epsit 0.01 ) : > / > Badly placed ()'s. > [areum@localhost 14]# > [areum@localhost 14]# [init] ========================= TP > 2 to TP 1 > ============================== > a > [init]: No match. > [areum@localhost 14]# Register TP 2 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > ) > Badly placed ()'s. > e > [areum@localhost 14]# to TP 1 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > ) > n > Badly placed ()'s. > [areum@localhost 14]# > [areum@localhost 14]# -- Original : (0.4688, > 0.4688, 0.800001) > mm size and (512, 512, 244) voxels. > Badly placed (. > [areum@localhost 14]# -- Resampled: (0.4688, > 0.4688, 0.4688) mm > size and (512, 512, 417) voxels. > Badly placed (. > [areum@localhost 14]# -- Reslicing using cubic bspline > a > --: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > T > MRItoBSpline: Command not found. > [areum@localhost 14]# -- Original : (0.4688, > 0.4688, 0.800001) > mm size and (512, 512, 244) voxels. > Badly placed (. > [areum@localhost 14]# -- Resampled: (0.4688, > 0.4688, 0.4688) mm > size and (512, 512, 417) voxels. > Badly placed (. > [areum@localhost 14]# -- Reslicing using cubic bspline > a > --: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > u > MRItoBSpline: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# - Max Resolution used: 3 > i > -: Command not found. > [areum@localhost 14]# -- gpS ( 64 , 64 , 52 ) > Badly placed ()'s. > [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) > Badly placed ()'s. > [areum@localhost 14]# - running loop to estimate saturation > parameter: > l > -: Command not found. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > 4 > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Killed > . > Killed: Command not found. > [areum@localhost 14]# Linux localhost.localdomain > 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 > x86_64 > x86_64 x86_64 GNU/Linux > > Linux: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# recon-all -s subj014 exited with > ERRORS at Sat > Oct 17 07:50:15 PDT 2015 > a > ERROR: Flag exited unrecognized. > -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 > 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s subj014 exited with ERRORS at Sat Oct 17 > 08:35:33 PDT > 2015 > > For more details, see the log file > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > [areum@localhost 14]# > [areum@localhost 14]# For more details, see the log file > > /usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log > > For: Command not found. > [areum@localhost 14]# To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > e > To: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# [areum@localhost 14]# recon-all -i > /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm -i > /usr/local/ > > [areum@localhost: Command not found. > [areum@localhost 14]# Subject Stamp: > freesurfer-Linux-centos6_x86_6 > i > Subject: Command not found. > [areum@localhost 14]# Current Stamp: > freesurfer-Linux-centos6_x8 > 2 > Current: Command not found. > [areum@localhost 14]# INFO: SUBJEC > INFO:: Too many arguments. > [areum@localhost 14]# Actual FREESURFER_HOME > /usr/local/freesurfer > 8 > Actual: Command not found. > [areum@localhost 14]# Linux localhost.l > s > Linux: Command not found. > [areum@localhost 14]# > /usr/local/freesurfer/subjects/OSA/14/subj014 > g > /usr/local/freesurfer/subjects/OSA/14/subj014: Permission > denied. > [areum@localhost 14]# > [areum@localhost 14]# mri_convert /u > mri_convert /u > > mri_convert: missing output volume name > > type mri_convert -u for usage > > [areum@localhost 14]# > [areum@localhost 14]# mri_convert > /usr/local/freesurfer/subjects/ > mri_convert /usr/local/freesurfer/subjects/ > > mri_convert: missing output volume name > > type mri_convert -u for usage > > [areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 > 2012/09/05 > 21:55:16 mreuter Exp $ > Bad : modifier in $ ( ). > [areum@localhost 14]# reading from > /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm... > reading: Command not found. > [areum@localhost 14]# Startin > Startin: Command not found. > [areum@localhost 14]# dcmfile = > /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm > dcmfile: Command not found. > [areum@localhost 14]# dcmdir = > /usr/local/freesurfer/subjects/OSA/14 > dcmdir: Command not found. > [areum@localhost 14]# Ref Series No = 3 > Ref: Command not found. > [areum@localhost 14]# Found 247 files, checking for dicoms > Found: Command not found. > [areum@localhost 14]# Found 244 dicom files in series. > Found: Command not found. > [areum@localhost 14]# First Sorting > First: Command not found. > [areum@localhost 14]# Computing Slice Direction > Computing: Command not found. > [areum@localhost 14]# Vs: -0.8 0 0 > Vs:: Too many arguments. > [areum@localhost 14]# Vs: -1 0 0 > Vs:: Too many arguments. > [areum@localhost 14]# Second Sorting > Second: Command not found. > [areum@localhost 14]# Counting frames > Counting: Command not found. > [areum@localhost 14]# nframes = 1 > nframes: Command not found. > [areum@localhost 14]# nslices = 244 > nslices: Command not found. > [areum@localhost 14]# ndcmfiles = 244 > ndcmfiles: Command not found. > [areum@localhost 14]# PE Dir = ROW (dicom read) > Badly placed ()'s. > [areum@localhost 14]# TransferSyntaxUID: > --1.2.840.10008.1.2.1-- > TransferSyntaxUID:: Too many arguments. > [areum@localhost 14]# Loading pixel data > Loading: Command not found. > [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip > angle=12.00 > TR=7.70,: Command not found. > [areum@localhost 14]# i_ras = (0, -1, 0) > Badly placed ()'s. > [areum@localhost 14]# j_ras = (0, 0, -1) > Badly placed ()'s. > [areum@localhost 14]# k_ras = (1, -0, 0) > Badly placed ()'s. > [areum@localhost 14]# writing to > /usr/local/freesurfer/subjects/OSA/14/subj014/ > writing: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# > [areum@localhost 14]# mri_convert > /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/loc > mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > /usr/loc > mri_convert: can't determine type of output volume > [areum@localhost 14]# > [areum@localhost 14]# mri_convert > /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > > mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm... > Starting DICOMRead2() > dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/14 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... > [areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 > 2012/09/05 > 21:55:16 mreuter Exp $ > Bad : modifier in $ ( ). > [areum@localhost 14]# reading from /usr/local/freesurfer/sub > reading: Command not found. > [areum@localhost 14]# Starting DICOMRead2() > Badly placed ()'s. > [areum@localhost 14]# dcmfile = > /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > dcmfile: Command not found. > [areum@localhost 14]# dcmdir = > /usr/local/freesurfer/subjects/OSA/14 > dcmdir: Command not found. > [areum@localhost 14]# Ref Series No = 3 > Ref: Command not found. > [areum@localhost 14]# Found 247 files, checking for dicoms > Found: Command not found. > [areum@localhost 14]# Found 244 di > Found: Command not found. > [areum@localhost 14]# First Sorting > First: Command not found. > [areum@localhost 14]# Computing Slice Direction > Computing: Command not found. > [areum@localhost 14]# Vs: -0.8 0 0 > Vs:: Too many arguments. > [areum@localhost 14]# Vs: -1 0 0 > Vs:: Too many arguments. > [areum@localhost 14]# Second Sorting > Second: Command not found. > [areum@localhost 14]# Counting frames > Counting: Command not found. > [areum@localhost 14]# nframes = 1 > nframes: Command not found. > [areum@localhost 14]# nslices = 244 > nslices: Command not found. > [areum@localhost 14]# ndcmfiles = 244 > ndcmfiles: Command not found. > [areum@localhost 14]# PE Dir = ROW (dicom read) > Badly placed ()'s. > [areum@localhost 14]# TransferSyntaxUID: > --1.2.840.10008.1.2.1-- > TransferSyntaxUID:: Too many arguments. > [areum@localhost 14]# Loading pixel data > Loading: Command not found. > [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip > angle=12.00 > TR=7.70,: Command not found. > [areum@localhost 14]# i_ras = (0, -1, 0) > Badly placed ()'s. > [areum@localhost 14]# j_ras = (0, 0, -1) > Badly placed ()'s. > [areum@localhost 14]# k_ras = (1, -0, 0) > Badly placed ()'s. > [areum@localhost 14]# writing to > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... > writing: Command not found. > [areum@localhost 14]# #---------------------------- > #----------------------------: Command not found. > [areum@localhost 14]# #@# MotionCor Sat Oct 17 08:09:23 > PDT 2015 > #@#: Command not found. > [areum@localhost 14]# Found 2 runs > Found: Command not found. > [areum@localhost 14]# > /usr/local/freesurfer/subjects/OSA/14/sub > /usr/local/freesurfer/subjects/OSA/14/sub: Command not found. > [areum@localhost 14]# /usr/local/freesurfer > /usr/local/freesurfer: Permission denied. > [areum@localhost 14]# Checking for (invalid) multi-frame > inputs... > Badly placed ()'s. > [areum@localhost 14]# Checking for (invalid) multi-frame in > Badly placed ()'s. > [areum@localhost 14]# > #----------------------------------------------- > #-----------------------------------------------: Command > not found. > [areum@localhost 14]# > /usr/local/freesurfer/subjects/OSA/14/subj014 > /usr/local/freesurfer/subjects/OSA/14/subj014: Permission > denied. > [areum@localhost 14]# > [areum@localhost 14]# > [areum@localhost 14]# > [areum@localhost 14]# $Id: mri_robust_temp > Bad : modifier in $ ( ). > [areum@localhost 14]# > [areum@localhost 14]# --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > as > movable/ > --mov:: Too many arguments. > [areum@localhost 14]# --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > a > --mov:: Too many arguments. > [areum@localhost 14]# Total: 2 input volumes > Total:: Too many arguments. > [areum@localhost 14]# --average: Using method 1 for template > computation. > --average:: Too many arguments. > [areum@localhost 14]# --template > --template: Command not found. > [areum@localhost 14]# --satit: Will estimate SAT iteratively! > --satit:: Too many arguments. > [areum@localhost 14]# --inittp: Using TP 1 as target for > initialization > --inittp:: Too many arguments. > [areum@localhost 14]# --fixtp: Will map everything to init TP! > --fixtp:: Too many arguments. > [areum@localhost 14]# --noit: Will output only first > template (no > iterations)! > Badly placed ()'s. > [areum@localhost 14]# --iscale: Enableing intensity scaling! > --iscale:: Too many arguments. > [areum@localhost 14]# --iscaleout: Will perform intensity > scaling and > output results > --iscaleout:: Too many arguments. > [areum@localhost 14]# --subsa > --subsa: Command not found. > [areum@localhost 14]# --lta: Will output LT > --lta:: Too many arguments. > [areum@localhost 14]# reading source > > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > reading: Command not found. > [areum@localhost 14]# converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > to > bspline ... > converting: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > MRItoBSpline: Command not found. > [areum@localhost 14]# rea > rea: Command not found. > [areum@localhost 14]# converting source '/u > Unmatched '. > [areum@localhost 14]# MRItoBSpline degree 3 > MRItoBSpline: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# Multi > Multi: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# [init] ========================= TP > 2 to TP 1 > ============================== > [init]: No match. > [areum@localhost 14]# Register TP 2 ( /usr/l > Too many ('s. > [areum@localhost 14]# to TP 1 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > ) > Badly placed ()'s. > [areum@localhost 14]# > [areum@localhost 14]# -- Original : (0.4688, > 0.4688, 0.800001) > mm size and (512, 512, 244) voxels. > Badly placed (. > [areum@localhost 14]# -- Resampled: (0.4688, > 0.4688, 0.4688) mm > size and (512, 512, 4 > Too many ('s. > [areum@localhost 14]# -- Reslicing using cubic bspline > --: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > MRItoBSpline: Command not found. > [areum@localhost 14]# -- Original : (0.4688, > 0.4688, 0.800001) > mm size and (512, 512, 244) voxels. > Badly placed (. > [areum@localhost 14]# -- Resampled: (0. > Too many ('s. > [areum@localhost 14]# -- Reslicing using cubic bspline > --: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > MRItoBSpline: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# - Max Resolution used: 3 > -: Command not found. > [areum@localhost 14]# -- gpS ( 64 , 64 , > Too many ('s. > [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) > Badly placed ()'s. > [areum@localhost 14]# - running loop to estimate > saturation pa > -: Command not found. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 > Sigma: Command not found. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical image > Too many ('s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: > Sigma: Command not found. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Si > Si: Command not found. > [areum@localhost 14]# Killed > Killed: Command not found. > [areum@localhost 14]# Linux localhost.localdomain 2.6.32 > Linux: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# recon-all -s subj014 exited with > ERRORS at Sat > Oct 17 08 > ERROR: Flag exited unrecognized. > -s subj014 exited with ERRORS at Sat Oct 17 08 > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 > 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s subj014 exited with ERRORS at Sat Oct 17 > 08:35:53 PDT > 2015 > > For more details, see the log file > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > how can i to do? > > plz help me.. > > 2015-10-18 0:11 GMT+09:00 Bruce Fischl > <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>: > Hi A-reum > > can you please follow the bug-reporting procedures in: > > https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > also, don't include a snapshot of text - cutting and > pasting the actual text in is far more useful, but in > addition we need a lot of other information if we are to > be able to help you > > cheers > Bruce > > On Sun, 18 Oct 2015, A-reum Min wrote: > > hello experts. > I have a question to you... > > I'm doing recon-all stage... but errors showed up > (fig.1) > > how can i to do? > > plz, help me > > > 2015-09-16 23:56 GMT+09:00 Douglas Greve > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>: > don't use .hdr. When you have a .hdr/.img > pair, just use the .img file. > > On 9/16/15 10:51 AM, A-reum Min wrote: > hello, experts > I have some question. > > I want to use analyze format instead of DICOM file. > > So, i type this sentence > > recon-all -i > /usr/local/freesurfer/subjects/test_han/I0071579.hdr > -i > /usr/local/freesurfer/subjects/test_han/I0071579.img > -all -s han001 > > > and then error occured.... > > ERROR: cannot determine file type for > /usr/local/freesurfer/subjects/test_han/I0071579.hdr > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 > SMP Wed Oct 15 > 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s han001 exited with ERRORS at Wed Sep 16 > 06:35:02 PDT 2015 > > For more details, see the log file > > /usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > How can i to do using analyze format? > > > 2015-08-27 23:55 GMT+09:00 Douglas N Greve > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>: > Specify something for --seg. It just needs to > be a surface > overlay of > the same size as the input. > > On 08/27/2015 01:49 AM, A-reum Min wrote: > > Hello doug > > > > i enter the ' mri_segstats --i y.mgh --vox > 33 0 0 --avgwf > out.dat' > > then, error occured --> ERROR: must specify > a segmentation > volume > > > > > > 2015-08-27 12:50 GMT+09:00 Douglas Greve > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>: > > > > don't use "vertexno", just put the > vertex number, eg, > --vox 33 0 0 > > > > > > On 8/26/15 9:22 PM, A-reum Min wrote: > >> Hello developer, > >> > >> I have some question to you. > >> > >> How can i get the significant vertices > value using Qdec > result? > >> > >> When i enter the 'mri_segstats --i > y.mgh --vox vertexno > 33 0 0 > >> --avgwf out.dat', then error ouccured > --> ERROR : > Option out.dat > >> unknown. > >> > >> So, i enter the 'mri_segstats --i y.mgh > --vox vertexno > 33 0 0 > >> --avgwf out.dat', then error occured > --> ERROR : Option > 0 unkown. > >> > >> How can i fix it? > >> > >> > >> > >> > >> > >> > >> > >> 2015-08-25 23:41 GMT+09:00 Douglas > Greve > >> <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>: > >> > >> > >> > >> On 8/25/15 9:35 AM, A-reum Min > wrote: > >>> Hello developers > >>> > >>> I have some question to you. > >>> > >>> 1.In fig.png, how many vertices > were composed of > cluster at > >>> least? > >> I'm not sure what you mean. it does > not look like > there are > >> any clusters there > >>> > >>> 2. How to change Area > Threshold(fig.png)? > >> The area is controlled by the > clusterwise threshold > (--cwp) > >> to mri_glmfit-sim > >>> > >>> 3. How to change CSD > thresh(fig.png)? > >> That is controlled by the threshold > when specifying > "--cache > >> threshold sign" to mri_glmfit-sim > >>> > >>> 4. What is the difference between > two words(Area > Threshold, > >>> CSD thresh)? > >> One is the cluster-pvalue and the > other is the > >> cluster-forming thershold > >>> > >>> 5. What is the exactly mean two > words(Area > Threshold, CSD > >>> thresh)? > >> See above > >> > >>> > >>> Thank you > >>> > >>> 2015-08-12 23:23 GMT+09:00 Douglas > N Greve > >>> <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>: > >>> > >>> > >>> > >>> On 08/10/2015 10:06 PM, A-reum > Min wrote: > >>> > HI expert ! > >>> > > >>> > My name is Areum. I have > some question to > you. > >>> > > >>> > 1. Does FreeSurfer offer a > effect size? if > that offer, > >>> how can i use > >>> > effect size? > >>> > > >>> If you're doing a group > analysis, you can > compute > >>> fscalc > glmdir/contrast/gamma.mgh div > glmdir/rstd.mgh -o > >>> glmdir/contrast/effectsize.mgh > >>> > > >>> > 2. I was wondering about the > stats.dat file > in > >>> stats_table (in Qdec > >>> > folder). > >>> > > >>> > Stats.dat file’s value mean > that each area’s > average > >>> (include whole > >>> > vertex) or each > >>> > > >>> > area’s average (only > significant vertex)? > >>> > > >>> what stats.dat? if > subject/stats/lh.aparc.stats, then > >>> the area is the > >>> total area for the ROI > >>> > > >>> > 3. Can I get whole vertex > value or > significant vertex > >>> value? Because, > >>> > I want to > >>> > > >>> > compare two groups > correlation using SPSS. In > >>> addition, I want to compare > >>> > > >>> > thickness, volume and > surface area > correlation within > >>> the one group > >>> > using SPSS. > >>> > > >>> You can extract a given vertex > with > >>> mri_segstats --i y.mgh --crs > vertexno 0 0 > --avgwf > >>> vertexno.dat > >>> vertexno.dat will be a text > file with number of > rows > >>> equalt to thge > >>> number of subjects where the > value is the data > from the > >>> given (0-based) > >>> vertex no. y.mgh is the input > to mri_glmfit > >>> > > >>> > 4. I currently use the > default cluster > >>> size(significant area > threshold > >>> > is 0mm^2). So, I > >>> > > >>> > want to control cluster size > larger than > default > >>> cluster size. How can > >>> > I control the > >>> > > >>> > cluster size? > >>> > > >>> I don't know what you mean. > >>> > > >>> > 5. In FreeSurfer manual, GLM > and Qdec have a > same > >>> results. But when I > >>> > use the > >>> > > >>> > both(GLM, Qdec) group > analysis program > results are not > >>> same. What is > >>> > differences > >>> > > >>> > between two analysis > program? How can I get > same > >>> result while GLM and > >>> > Qdec? > >>> > > >>> No way to know unless you tell > us the specifics > of what > >>> you did > >>> > > >>> > 6. How can I get surface > area and volume > using > >>> GLM(group analysis > >>> > program)? > >>> > > >>> surface area and volume are > outputs of > recon-all, not glm > >>> > > >>> > > >>> > plz reply to me > >>> > > >>> > > >>> > 2015-08-10 21:35 GMT+09:00 > A-reum Min > >>> <naniy...@gmail.com > <mailto:naniy...@gmail.com> > <mailto:naniy...@gmail.com <mailto:naniy...@gmail.com>> > >>> > <mailto:naniy...@gmail.com > <mailto:naniy...@gmail.com> > <mailto:naniy...@gmail.com > <mailto:naniy...@gmail.com>>>>: > >>> > > >>> > Hello developer~ > >>> > > >>> > I have some questions to you. > >>> > > >>> > 1. Does FreeSurfer offer a > effect size? if that > >>> offer, how can i > >>> > use effect size? > >>> > > >>> > 2. I was wondering about the > stats.dat file in > >>> stats_table (in > >>> > Qdec folder). > >>> > > >>> > Stats.dat file’s value mean > that each area’s > >>> average (include > >>> > whole vertex) or each > >>> > > >>> > area’s average (only > significant vertex)? > >>> > > >>> > 3. Can I get whole vertex > value or significant > >>> vertex value? > >>> > Because, I want to > >>> > > >>> > compare two groups correlation > using SPSS. In > >>> addition, I want to > >>> > compare > >>> > > >>> > thickness, volume and surface > area correlation > >>> within the one > >>> > group using SPSS. > >>> > > >>> > 4. I currently use the default > cluster > >>> size(significant area > >>> > threshold is 0mm^2). So, I > >>> > > >>> > want to control cluster size > larger than > default > >>> cluster size. How > >>> > can I control the > >>> > > >>> > cluster size? > >>> > > >>> > 5. In FreeSurfer manual, GLM > and Qdec have a > same > >>> results. But > >>> > when I use the > >>> > > >>> > both(GLM, Qdec) group analysis > program results > are > >>> not same. What > >>> > is differences > >>> > > >>> > between two analysis program? > How can I get > same > >>> result while GLM > >>> > and Qdec? > >>> > > >>> > 6. How can I get surface area > and volume using > >>> GLM(group analysis > >>> > program)? > >>> > > >>> > > >>> > thanks for your help > >>> > > >>> > > >>> > 2015-07-27 14:28 GMT+09:00 > A-reum Min > >>> <naniy...@gmail.com > <mailto:naniy...@gmail.com> > <mailto:naniy...@gmail.com <mailto:naniy...@gmail.com>> > >>> > <mailto:naniy...@gmail.com > <mailto:naniy...@gmail.com> > >>> <mailto:naniy...@gmail.com > <mailto:naniy...@gmail.com>>>>: > >>> > > >>> > Hello bruce > >>> > > >>> > I solve this > problem(12.png) > >>> > > >>> > Thank you > >>> > > >>> > 2015-07-27 13:03 GMT+09:00 > dgw > >>> <dgwake...@gmail.com > <mailto:dgwake...@gmail.com> > <mailto:dgwake...@gmail.com > <mailto:dgwake...@gmail.com>> > >>> > > <mailto:dgwake...@gmail.com > <mailto:dgwake...@gmail.com> > >>> <mailto:dgwake...@gmail.com > <mailto:dgwake...@gmail.com>>>>: > >>> > > >>> > Hi A-reum, > >>> > > >>> > I think you may be > able to get a faster > >>> response if you > >>> > include some > >>> > details about your > setup: I would start > >>> with the following: > >>> > > >>> > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >>> > and run bugr. > >>> > > >>> > hth > >>> > D > >>> > > >>> > On 7/26/15 5:17 PM, > A-reum Min wrote: > >>> > > Hi, Bruce > >>> > > > >>> > > When i use a Qdec, > this > message(12.png) > >>> show up.. > >>> > > How can i solve this > problem? > >>> > > > >>> > > 2015-07-23 22:57 > GMT+09:00 Bruce > Fischl > >>> > > <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > >>> <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>> > >>> > > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > >>> <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>> > >>> > > > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > >>> <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>> > >>> > > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > >>> > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>>>>: > >>> > > > >>> > > 1. No, each > subject has a > different > >>> #. You can map > >>> > to fsaverage > >>> > > (this is what > -qcache does if you > >>> specify it for > >>> > recon-all), then > >>> > > they will have > the same #. > >>> > > > >>> > > 2. What result > data do you mean? > >>> > > > >>> > > 3. Yes, although > I'll leave the > >>> details to Doug > >>> > (since I don't > >>> > > remember how his > cluster code > works). > >>> > > > >>> > > 4. The > significance doesn't > depend > >>> on the cluster > >>> > size unless you do > >>> > > multiple comparison > corrections (and > >>> even then only > >>> > if you do them a > >>> > > certain way) > >>> > > > >>> > > cheers > >>> > > Bruce > >>> > > > >>> > > > >>> > > On Thu, 23 Jul > 2015, A-reum Min > wrote: > >>> > > > >>> > > HELLO developer > >>> > > I have some > question to you.. > >>> > > > >>> > > 1. Every > patient is given to the > >>> same number > >>> > of vertex? > >>> > > > >>> > > 2. When i use a > Qdec, How can I > get the > >>> > subject result data? > >>> > > > >>> > > 3. Could i get > the significant > vertex’s > >>> > number, extent of the > >>> > > significant area > and gray matter > volume? > >>> > > > >>> > > 4. Is it > significant blue color > >>> which how > >>> > many connected > >>> > > vertex? > >>> > > > >>> > > > >>> > > 2015-05-29 2:03 > GMT+09:00 A-reum Min > >>> > <naniy...@gmail.com > <mailto:naniy...@gmail.com> > >>> <mailto:naniy...@gmail.com > <mailto:naniy...@gmail.com>> > <mailto:naniy...@gmail.com <mailto:naniy...@gmail.com> > >>> <mailto:naniy...@gmail.com > <mailto:naniy...@gmail.com>>> > >>> > > > <mailto:naniy...@gmail.com <mailto:naniy...@gmail.com> > >>> <mailto:naniy...@gmail.com > <mailto:naniy...@gmail.com>> > >>> > > <mailto:naniy...@gmail.com <mailto:naniy...@gmail.com> > <mailto:naniy...@gmail.com > <mailto:naniy...@gmail.com>>>>>: > >>> > > hello developer~ > >>> > > reconstruction is > well done, so i'm > >>> doing on > >>> > 'qdec' step.. > >>> > > Actually, i don't > know how to treat > the > >>> Design > >>> > menu exactly.. > >>> > > > >>> > > >>> > > -------------------------------------------------------------------------- > - > >>> > > Discrete(fixed > factors) : diagnosis > >>> > > continuous > (covariate) : age , > >>> > Left-Lateral-Ventricle > >>> > > > >>> > > >>> > > -------------------------------------------------------------------------- > - > >>> > > which one click > before analyze? > >>> > > > >>> > > age range is > 12years~24years/ > >>> > > all subjects > are adolescent. > >>> > > and no > outlier in age range.. > >>> so.. age > >>> > (continuous factor) > does not > >>> > > nasessart? > >>> > > > >>> > > > >>> > > 2015-05-29 1:19 > GMT+09:00 A-reum Min > >>> > <naniy...@gmail.com > <mailto:naniy...@gmail.com> > >>> <mailto:naniy...@gmail.com > <mailto:naniy...@gmail.com>> > <mailto:naniy...@gmail.com <mailto:naniy...@gmail.com> > >>> <mailto:naniy...@gmail.com > <mailto:naniy...@gmail.com>>> > >>> > > > <mailto:naniy...@gmail.com <mailto:naniy...@gmail.com> > >>> <mailto:naniy...@gmail.com > <mailto:naniy...@gmail.com>> > >>> > > <mailto:naniy...@gmail.com <mailto:naniy...@gmail.com> > <mailto:naniy...@gmail.com > <mailto:naniy...@gmail.com>>>>>: > >>> > > hello developer~ > >>> > > reconstruction is > well done, so i'm > >>> doing on > >>> > 'qdec' step.. > >>> > > Actually, i don't > know how to treat > the > >>> Design > >>> > menu exactly.. > >>> > > > >>> > > >>> > > -------------------------------------------------------------------------- > - > >>> > > Discrete(fixed > factors) : diagnosis > >>> > > continuous > (covariate) : age , > >>> > Left-Lateral-Ventricle > >>> > > > >>> > > >>> > > -------------------------------------------------------------------------- > - > >>> > > which one click > before analyze? > >>> > > > >>> > > > >>> > > > >>> > > 2015-04-05 21:41 > GMT+09:00 Bruce > Fischl > >>> > > > <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > >>> <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>> > >>> > > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > >>> <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>> > >>> > > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > >>> <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>> > >>> > > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > >>> > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>>>>: > >>> > > I'm glad it worked > out > >>> > > Bruce > >>> > > On Sun, 5 Apr > 2015, A-reum Min > wrote: > >>> > > > >>> > > Hello Bruce~ > >>> > > You're > right.. my PISA dicom > file > >>> > header > >>> > > is too short > >>> > > so, > freesurfer didn't read > it. > >>> > > > >>> > > Therefore I > use another > subjects > >>> dicom > >>> > > file and > then freesurfer read > it! > >>> > > > >>> > > thank you > for u r adavice to > me. > >>> > > > >>> > > I really > appreciate u > >>> > > > >>> > > 2015-04-05 > 7:08 GMT+09:00 > Bruce > >>> Fischl > >>> > > > <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > >>> <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>> > >>> > > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > >>> <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>> > >>> > > > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > >>> <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person > to whom it is > addressed. If you believe this e-mail was sent to you in error > and the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was > sent to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
