Hello expert. I'm Areum.
I have some question to you. A weeks ago, i compared two groups (OSA patients VS control) and then the number of vertices were confirmed. Each group has the same number of vertices.(176416) -experiment 1. And yesterday, i compared two groups(partial sleep deprivation:PSD VS control) and then the number of vertices were confirmed. Each group has the same number of vertices(169548) -experiment 2. 1) Why isn't the same number of total vertices? is it related brain size? 2) How can i extract the number of total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(PSD) and average of PSD ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex). plz answer me. Thank you. 2016-01-16 23:39 GMT+09:00 A-reum Min <naniy...@gmail.com>: > Hello expert. > > I'm Areum. > > I have some question to you. > > A weeks ago, i compared two groups (OSA patients VS control) and then the > number of vertices were confirmed. > > Each group has the same number of vertices.(176416) -experiment 1. > > And yesterday, i compared two groups(partial sleep deprivation:PSD VS > control) and then the number of vertices were confirmed. > > Each group has the same number of vertices(169548) -experiment 2. > > > 1) Why isn't the same number of total vertices? is it related rain size? > > > 2) How can i extract the number of total vertices(ex.#1 vertex : cortical > thickness value) to 1 subject(PSD) and average of PSD ? > I want to compared asymmetry of brain (lateralization). So, i really > necessary above value(cortical thickness value of vertex). > > plz answer me. > > Thank you. > > > 2016-01-07 3:52 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > >> 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 <fis...@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 >>> <naniy...@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 >>> <gr...@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 >>> <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/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 >>> <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]# >>> > >> >> >> _______________________________________________ >> 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. 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. >> >> > > > -- > *------------------------------------------------------------* > *Areum Min* > Medical Image Processing Lab. > Department of Biomedical Engineering, Yonsei Univ. > 218 San-hak Hall, 1 Yeonsedae-gil, Heungeop-myeon, Wonju, Gangwon, Korea > Office : +82-33-760-2499 > Mobile : +82-10-3428-0608 > E-Mail : n <esth...@nate.com>aniy...@gmail.com > -- *------------------------------------------------------------* *Areum Min* Medical Image Processing Lab. Department of Biomedical Engineering, Yonsei Univ. 218 San-hak Hall, 1 Yeonsedae-gil, Heungeop-myeon, Wonju, Gangwon, Korea Office : +82-33-760-2499 Mobile : +82-10-3428-0608 E-Mail : n <esth...@nate.com>aniy...@gmail.com
_______________________________________________ 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. 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.
