6 Jan
2016
6 Jan
'16
1:52 p.m.
Hi A-reum
did you talk to the Wash U group? If you have nifti files they can be processed using recon-all (i.e. recon-all -i <full path to nifti file> -s <subject id> -sd <directory to contain all subjects> -all)
cheers Bruce
On Tue, 29 Dec 2015, A-reum Min wrote:
hello experts!my name is areum. i have some question to you.i have never seen before these NIFTI format(fig.1.png) I want to see these data subjects's cortical thickness using qdec. how can i to do? plz answer me
2015-12-25 2:16 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi A-reum
you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce On Thu, 24 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-11-10 7:49 GMT+09:00 A-reum Min <naniyaah@gmail.com>: Hello experts! I have some question to you.. I don't need to show up so small blue regions(fig.1 blue region) How can i control these? 2015-11-10 7:41 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>: Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate. On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... > #-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... > #----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > --average 1 --template > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/0 0 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.t x t > --subsample 200 --lta > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta > > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > as > movable/source volume. > --mov: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > ) > to TP 1 ( > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > > - Max Resolution used: 3 > -- gpS ( 64 , 64 , 52 ) > -- gpT ( 64 , 64 , 52 ) > - running loop to estimate saturation parameter: > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Killed > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s sub002 exited with ERRORS at Thu Nov 5 > 02:37:57 PST 2015 > > For more details, see the log file > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > 2015-10-19 11:05 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > hello experts. > i have a question to you.. > > i'm doing recon-all stage, but errors show up like this > > > > > ects/OSA/14/subj014/mri/orig/002.mgz --average 1 --template > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale --iscaleout > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt > --subsample 200 --lta > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta > > / > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter > Exp $ > > --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > as > movable/source volume. > --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 > , epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > ) > to TP 1 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, > 244) voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, > 417) voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, > 244) voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, > 417) voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > > - Max Resolution used: 3 > -- gpS ( 64 , 64 , 52 ) > -- gpT ( 64 , 64 , 52 ) > - running loop to estimate saturation parameter: > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Killed > [areum@localhost 14]# > > [areum@localhost 14]# $Id: mri_robust_template.cpp,v 1.37.2.2 > 2012/10/10 19:59:06 mreuter Exp $ > c > Bad : modifier in $ ( ). > [areum@localhost 14]# > [areum@localhost 14]# --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > as > movable/source volume. > --mov:: Too many arguments. > [areum@localhost 14]# --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > as > movable/source volume. > --mov:: Too many arguments. > [areum@localhost 14]# Total: 2 input volumes > Total:: Too many arguments. > b > [areum@localhost 14]# --average: Using method 1 for template > computation. > --average:: Too many arguments. > [areum@localhost 14]# --template: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > as > template output volume. > --template:: Too many arguments. > [areum@localhost 14]# --satit: Will estimate SAT iteratively! > i > --satit:: Too many arguments. > [areum@localhost 14]# --inittp: Using TP 1 as target for > initialization > --inittp:: Too many arguments. > [areum@localhost 14]# --fixtp: Will map everything to init TP! > --fixtp:: Too many arguments. > [areum@localhost 14]# --noit: Will output only first > template (no > iterations)! > Badly placed ()'s. > [areum@localhost 14]# --iscale: Enableing intensity scaling! > --iscale:: Too many arguments. > [areum@localhost 14]# --iscaleout: Will perform intensity > scaling and > output results > --iscaleout:: Too many arguments. > [areum@localhost 14]# --subsample: Will subsample if size > is larger > than 200 on all axes! > --subsample:: Too many arguments. > [areum@localhost 14]# --lta: Will output LTA transforms > --lta:: Too many arguments. > [areum@localhost 14]# reading source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > - > reading: Command not found. > [areum@localhost 14]# converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > to > bspline ... > b > converting: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > r > MRItoBSpline: Command not found. > [areum@localhost 14]# reading source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... > n > reading: Command not found. > [areum@localhost 14]# converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' > to > bspline ... > > converting: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > p > MRItoBSpline: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# MultiRegistration::initializing > Xforms (init 1 , > maxres 0 , iterate 5 , epsit 0.01 ) : > / > Badly placed ()'s. > [areum@localhost 14]# > [areum@localhost 14]# [init] ========================= TP > 2 to TP 1 > ============================== > a > [init]: No match. > [areum@localhost 14]# Register TP 2 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > ) > Badly placed ()'s. > e > [areum@localhost 14]# to TP 1 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > ) > n > Badly placed ()'s. > [areum@localhost 14]# > [areum@localhost 14]# -- Original : (0.4688, > 0.4688, 0.800001) > mm size and (512, 512, 244) voxels. > Badly placed (. > [areum@localhost 14]# -- Resampled: (0.4688, > 0.4688, 0.4688) mm > size and (512, 512, 417) voxels. > Badly placed (. > [areum@localhost 14]# -- Reslicing using cubic bspline > a > --: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > T > MRItoBSpline: Command not found. > [areum@localhost 14]# -- Original : (0.4688, > 0.4688, 0.800001) > mm size and (512, 512, 244) voxels. > Badly placed (. > [areum@localhost 14]# -- Resampled: (0.4688, > 0.4688, 0.4688) mm > size and (512, 512, 417) voxels. > Badly placed (. > [areum@localhost 14]# -- Reslicing using cubic bspline > a > --: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > u > MRItoBSpline: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# - Max Resolution used: 3 > i > -: Command not found. > [areum@localhost 14]# -- gpS ( 64 , 64 , 52 ) > Badly placed ()'s. > [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) > Badly placed ()'s. > [areum@localhost 14]# - running loop to estimate saturation > parameter: > l > -: Command not found. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > 4 > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Killed > . > Killed: Command not found. > [areum@localhost 14]# Linux localhost.localdomain > 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 > x86_64 > x86_64 x86_64 GNU/Linux > > Linux: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# recon-all -s subj014 exited with > ERRORS at Sat > Oct 17 07:50:15 PDT 2015 > a > ERROR: Flag exited unrecognized. > -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 > 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s subj014 exited with ERRORS at Sat Oct 17 > 08:35:33 PDT > 2015 > > For more details, see the log file > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > [areum@localhost 14]# > [areum@localhost 14]# For more details, see the log file > /usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log > > For: Command not found. > [areum@localhost 14]# To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > e > To: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# [areum@localhost 14]# recon-all -i > /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm -i > /usr/local/ > > [areum@localhost: Command not found. > [areum@localhost 14]# Subject Stamp: > freesurfer-Linux-centos6_x86_6 > i > Subject: Command not found. > [areum@localhost 14]# Current Stamp: > freesurfer-Linux-centos6_x8 > 2 > Current: Command not found. > [areum@localhost 14]# INFO: SUBJEC > INFO:: Too many arguments. > [areum@localhost 14]# Actual FREESURFER_HOME > /usr/local/freesurfer > 8 > Actual: Command not found. > [areum@localhost 14]# Linux localhost.l > s > Linux: Command not found. > [areum@localhost 14]# > /usr/local/freesurfer/subjects/OSA/14/subj014 > g > /usr/local/freesurfer/subjects/OSA/14/subj014: Permission > denied. > [areum@localhost 14]# > [areum@localhost 14]# mri_convert /u > mri_convert /u > > mri_convert: missing output volume name > > type mri_convert -u for usage > > [areum@localhost 14]# > [areum@localhost 14]# mri_convert > /usr/local/freesurfer/subjects/ > mri_convert /usr/local/freesurfer/subjects/ > > mri_convert: missing output volume name > > type mri_convert -u for usage > > [areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 > 2012/09/05 > 21:55:16 mreuter Exp $ > Bad : modifier in $ ( ). > [areum@localhost 14]# reading from > /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm... > reading: Command not found. > [areum@localhost 14]# Startin > Startin: Command not found. > [areum@localhost 14]# dcmfile = > /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm > dcmfile: Command not found. > [areum@localhost 14]# dcmdir = > /usr/local/freesurfer/subjects/OSA/14 > dcmdir: Command not found. > [areum@localhost 14]# Ref Series No = 3 > Ref: Command not found. > [areum@localhost 14]# Found 247 files, checking for dicoms > Found: Command not found. > [areum@localhost 14]# Found 244 dicom files in series. > Found: Command not found. > [areum@localhost 14]# First Sorting > First: Command not found. > [areum@localhost 14]# Computing Slice Direction > Computing: Command not found. > [areum@localhost 14]# Vs: -0.8 0 0 > Vs:: Too many arguments. > [areum@localhost 14]# Vs: -1 0 0 > Vs:: Too many arguments. > [areum@localhost 14]# Second Sorting > Second: Command not found. > [areum@localhost 14]# Counting frames > Counting: Command not found. > [areum@localhost 14]# nframes = 1 > nframes: Command not found. > [areum@localhost 14]# nslices = 244 > nslices: Command not found. > [areum@localhost 14]# ndcmfiles = 244 > ndcmfiles: Command not found. > [areum@localhost 14]# PE Dir = ROW (dicom read) > Badly placed ()'s. > [areum@localhost 14]# TransferSyntaxUID: > --1.2.840.10008.1.2.1-- > TransferSyntaxUID:: Too many arguments. > [areum@localhost 14]# Loading pixel data > Loading: Command not found. > [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip > angle=12.00 > TR=7.70,: Command not found. > [areum@localhost 14]# i_ras = (0, -1, 0) > Badly placed ()'s. > [areum@localhost 14]# j_ras = (0, 0, -1) > Badly placed ()'s. > [areum@localhost 14]# k_ras = (1, -0, 0) > Badly placed ()'s. > [areum@localhost 14]# writing to > /usr/local/freesurfer/subjects/OSA/14/subj014/ > writing: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# > [areum@localhost 14]# mri_convert > /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/loc > mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > /usr/loc > mri_convert: can't determine type of output volume > [areum@localhost 14]# > [areum@localhost 14]# mri_convert > /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > > mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm... > Starting DICOMRead2() > dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/14 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... > [areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 > 2012/09/05 > 21:55:16 mreuter Exp $ > Bad : modifier in $ ( ). > [areum@localhost 14]# reading from /usr/local/freesurfer/sub > reading: Command not found. > [areum@localhost 14]# Starting DICOMRead2() > Badly placed ()'s. > [areum@localhost 14]# dcmfile = > /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > dcmfile: Command not found. > [areum@localhost 14]# dcmdir = > /usr/local/freesurfer/subjects/OSA/14 > dcmdir: Command not found. > [areum@localhost 14]# Ref Series No = 3 > Ref: Command not found. > [areum@localhost 14]# Found 247 files, checking for dicoms > Found: Command not found. > [areum@localhost 14]# Found 244 di > Found: Command not found. > [areum@localhost 14]# First Sorting > First: Command not found. > [areum@localhost 14]# Computing Slice Direction > Computing: Command not found. > [areum@localhost 14]# Vs: -0.8 0 0 > Vs:: Too many arguments. > [areum@localhost 14]# Vs: -1 0 0 > Vs:: Too many arguments. > [areum@localhost 14]# Second Sorting > Second: Command not found. > [areum@localhost 14]# Counting frames > Counting: Command not found. > [areum@localhost 14]# nframes = 1 > nframes: Command not found. > [areum@localhost 14]# nslices = 244 > nslices: Command not found. > [areum@localhost 14]# ndcmfiles = 244 > ndcmfiles: Command not found. > [areum@localhost 14]# PE Dir = ROW (dicom read) > Badly placed ()'s. > [areum@localhost 14]# TransferSyntaxUID: > --1.2.840.10008.1.2.1-- > TransferSyntaxUID:: Too many arguments. > [areum@localhost 14]# Loading pixel data > Loading: Command not found. > [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip > angle=12.00 > TR=7.70,: Command not found. > [areum@localhost 14]# i_ras = (0, -1, 0) > Badly placed ()'s. > [areum@localhost 14]# j_ras = (0, 0, -1) > Badly placed ()'s. > [areum@localhost 14]# k_ras = (1, -0, 0) > Badly placed ()'s. > [areum@localhost 14]# writing to > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... > writing: Command not found. > [areum@localhost 14]# #---------------------------- > #----------------------------: Command not found. > [areum@localhost 14]# #@# MotionCor Sat Oct 17 08:09:23 > PDT 2015 > #@#: Command not found. > [areum@localhost 14]# Found 2 runs > Found: Command not found. > [areum@localhost 14]# > /usr/local/freesurfer/subjects/OSA/14/sub > /usr/local/freesurfer/subjects/OSA/14/sub: Command not found. > [areum@localhost 14]# /usr/local/freesurfer > /usr/local/freesurfer: Permission denied. > [areum@localhost 14]# Checking for (invalid) multi-frame > inputs... > Badly placed ()'s. > [areum@localhost 14]# Checking for (invalid) multi-frame in > Badly placed ()'s. > [areum@localhost 14]# > #----------------------------------------------- > #-----------------------------------------------: Command > not found. > [areum@localhost 14]# > /usr/local/freesurfer/subjects/OSA/14/subj014 > /usr/local/freesurfer/subjects/OSA/14/subj014: Permission > denied. > [areum@localhost 14]# > [areum@localhost 14]# > [areum@localhost 14]# > [areum@localhost 14]# $Id: mri_robust_temp > Bad : modifier in $ ( ). > [areum@localhost 14]# > [areum@localhost 14]# --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > as > movable/ > --mov:: Too many arguments. > [areum@localhost 14]# --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > a > --mov:: Too many arguments. > [areum@localhost 14]# Total: 2 input volumes > Total:: Too many arguments. > [areum@localhost 14]# --average: Using method 1 for template > computation. > --average:: Too many arguments. > [areum@localhost 14]# --template > --template: Command not found. > [areum@localhost 14]# --satit: Will estimate SAT iteratively! > --satit:: Too many arguments. > [areum@localhost 14]# --inittp: Using TP 1 as target for > initialization > --inittp:: Too many arguments. > [areum@localhost 14]# --fixtp: Will map everything to init TP! > --fixtp:: Too many arguments. > [areum@localhost 14]# --noit: Will output only first > template (no > iterations)! > Badly placed ()'s. > [areum@localhost 14]# --iscale: Enableing intensity scaling! > --iscale:: Too many arguments. > [areum@localhost 14]# --iscaleout: Will perform intensity > scaling and > output results > --iscaleout:: Too many arguments. > [areum@localhost 14]# --subsa > --subsa: Command not found. > [areum@localhost 14]# --lta: Will output LT > --lta:: Too many arguments. > [areum@localhost 14]# reading source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > reading: Command not found. > [areum@localhost 14]# converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > to > bspline ... > converting: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > MRItoBSpline: Command not found. > [areum@localhost 14]# rea > rea: Command not found. > [areum@localhost 14]# converting source '/u > Unmatched '. > [areum@localhost 14]# MRItoBSpline degree 3 > MRItoBSpline: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# Multi > Multi: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# [init] ========================= TP > 2 to TP 1 > ============================== > [init]: No match. > [areum@localhost 14]# Register TP 2 ( /usr/l > Too many ('s. > [areum@localhost 14]# to TP 1 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > ) > Badly placed ()'s. > [areum@localhost 14]# > [areum@localhost 14]# -- Original : (0.4688, > 0.4688, 0.800001) > mm size and (512, 512, 244) voxels. > Badly placed (. > [areum@localhost 14]# -- Resampled: (0.4688, > 0.4688, 0.4688) mm > size and (512, 512, 4 > Too many ('s. > [areum@localhost 14]# -- Reslicing using cubic bspline > --: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > MRItoBSpline: Command not found. > [areum@localhost 14]# -- Original : (0.4688, > 0.4688, 0.800001) > mm size and (512, 512, 244) voxels. > Badly placed (. > [areum@localhost 14]# -- Resampled: (0. > Too many ('s. > [areum@localhost 14]# -- Reslicing using cubic bspline > --: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > MRItoBSpline: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# - Max Resolution used: 3 > -: Command not found. > [areum@localhost 14]# -- gpS ( 64 , 64 , > Too many ('s. > [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) > Badly placed ()'s. > [areum@localhost 14]# - running loop to estimate > saturation pa > -: Command not found. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 > Sigma: Command not found. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical image > Too many ('s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: > Sigma: Command not found. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Si > Si: Command not found. > [areum@localhost 14]# Killed > Killed: Command not found. > [areum@localhost 14]# Linux localhost.localdomain 2.6.32 > Linux: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# recon-all -s subj014 exited with > ERRORS at Sat > Oct 17 08 > ERROR: Flag exited unrecognized. > -s subj014 exited with ERRORS at Sat Oct 17 08 > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 > 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s subj014 exited with ERRORS at Sat Oct 17 > 08:35:53 PDT > 2015 > > For more details, see the log file > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > how can i to do? > > plz help me.. > > 2015-10-18 0:11 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>: > Hi A-reum > > can you please follow the bug-reporting procedures in: > > https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > also, don't include a snapshot of text - cutting and > pasting the actual text in is far more useful, but in > addition we need a lot of other information if we are to > be able to help you > > cheers > Bruce > > On Sun, 18 Oct 2015, A-reum Min wrote: > > hello experts. > I have a question to you... > > I'm doing recon-all stage... but errors showed up > (fig.1) > > how can i to do? > > plz, help me > > > 2015-09-16 23:56 GMT+09:00 Douglas Greve > <greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>: > don't use .hdr. When you have a .hdr/.img > pair, just use the .img file. > > On 9/16/15 10:51 AM, A-reum Min wrote: > hello, experts > I have some question. > > I want to use analyze format instead of DICOM file. > > So, i type this sentence > > recon-all -i > /usr/local/freesurfer/subjects/test_han/I0071579.hdr > -i > /usr/local/freesurfer/subjects/test_han/I0071579.img > -all -s han001 > > > and then error occured.... > > ERROR: cannot determine file type for > /usr/local/freesurfer/subjects/test_han/I0071579.hdr > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 > SMP Wed Oct 15 > 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s han001 exited with ERRORS at Wed Sep 16 > 06:35:02 PDT 2015 > > For more details, see the log file > /usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > How can i to do using analyze format? > > > 2015-08-27 23:55 GMT+09:00 Douglas N Greve > <greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>: > Specify something for --seg. It just needs to > be a surface > overlay of > the same size as the input. > > On 08/27/2015 01:49 AM, A-reum Min wrote: > > Hello doug > > > > i enter the ' mri_segstats --i y.mgh --vox > 33 0 0 --avgwf > out.dat' > > then, error occured --> ERROR: must specify > a segmentation > volume > > > > > > 2015-08-27 12:50 GMT+09:00 Douglas Greve > <greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>: > > > > don't use "vertexno", just put the > vertex number, eg, > --vox 33 0 0 > > > > > > On 8/26/15 9:22 PM, A-reum Min wrote: > >> Hello developer, > >> > >> I have some question to you. > >> > >> How can i get the significant _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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