Freesurfer January 2016

freesurfer@nmr.mgh.harvard.edu

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204 discussions

Cannot open FreeSurfer application zipped file
by Meirelles, Osorio (NIH/NIA/IRP) [E] 27 Jan '16

27 Jan '16

Dear experts, I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder. I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file” Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated. Thanks, Osorio -----Original Message----- From: Meirelles, Osorio (NIH/NIA/IRP) [E] Sent: Thursday, December 24, 2015 12:23 PM To: Freesurfer support list Cc: Matthew Glasser Subject: RE: [Freesurfer] hello freesurfer developer~ Dear experts, I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder. I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file” Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated. Thanks, Osorio -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 24, 2015 12:16 PM To: Freesurfer support list Cc: Matthew Glasser Subject: Re: [Freesurfer] hello freesurfer developer~ Hi A-reum you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce On Thu, 24 Dec 2015, A-reum Min wrote: > hello experts!my name is areum. > i have some question to you. > a few days ago i was down load HCP(human connectom project) data. > but.. how can i use these HCP format. > i have never seen before these format(fig.1.png) > I want to see HCP data subjects's cortical thickness using qdec. > how can i to do? > plz answer me > > 2015-11-10 7:49 GMT+09:00 A-reum Min <naniyaah(a)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(a)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(a)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(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>: > > > > are > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > > and > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > > images from *different* series or from the > *same* series? If > > they are in the same series than that explains > what is > > happening. You should only give recon-all a > single file from > > any one acquisition - it will figure out the > rest of the files > > that are part of it. > > > > cheers > > Bruce > > > > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > > > hello experts. > > i have some question to you... > > > > when i enter the recon-all -i /paht~ > > > > error showed up.... like below one.. > > > > how can i to fix it? > > > > [areum@localhost 0165766_1]# recon-all -i > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > -i > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > > -all -s sub002 > > Subject Stamp: > > > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > Current Stamp: > > > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > INFO: SUBJECTS_DIR is > > /usr/local/freesurfer/subjects/OSA/0165766_1 > > Actual FREESURFER_HOME /usr/local/freesurfer > > Linux localhost.localdomain > 2.6.32-504.el6.x86_64 #1 SMP > > Wed Oct 15 04:27:16 > > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > > > mri_convert > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > > > > mri_convert > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 > 21:55:16 mreuter > > Exp $ > > reading from > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > > Starting DICOMRead2() > > dcmfile = > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > > dcmdir = > /usr/local/freesurfer/subjects/OSA/0165766_1 > > Ref Series No = 3 > > Found 247 files, checking for dicoms > > Found 244 dicom files in series. > > First Sorting > > Computing Slice Direction > > Vs: -0.8 0 0 > > Vs: -1 0 0 > > Second Sorting > > Counting frames > > nframes = 1 > > nslices = 244 > > ndcmfiles = 244 > > PE Dir = ROW (dicom read) > > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > > Loading pixel data > > TR=7.70, TE=3.37, TI=400.00, flip > angle=12.00 > > i_ras = (0, -1, 0) > > j_ras = (0, 0, -1) > > k_ras = (1, -0, 0) > > writing to > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > > > mri_convert > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > > > > mri_convert > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 > 21:55:16 mreuter > > Exp $ > > reading from > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > > Starting DICOMRead2() > > dcmfile = > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > > dcmdir = > /usr/local/freesurfer/subjects/OSA/0165766_1 > > Ref Series No = 3 > > Found 247 files, checking for dicoms > > Found 244 dicom files in series. > > First Sorting > > Computing Slice Direction > > Vs: -0.8 0 0 > > Vs: -1 0 0 > > Second Sorting > > Counting frames > > nframes = 1 > > nslices = 244 > > ndcmfiles = 244 > > PE Dir = ROW (dicom read) > > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > > Loading pixel data > > TR=7.70, TE=3.37, TI=400.00, flip > angle=12.00 > > i_ras = (0, -1, 0) > > j_ras = (0, 0, -1) > > k_ras = (1, -0, 0) > > writing to > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... > > > #-------------------------------------------- > > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > > Found 2 runs > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > Checking for (invalid) multi-frame inputs... > > Checking for (invalid) multi-frame inputs... > > > #----------------------------------------------- > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > > > mri_robust_template --mov > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > --average 1 --template > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > > --satit > > --inittp 1 --fixtp --noit --iscale > > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/00 > 1-iscale.txt > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.tx > t > > --subsample 200 --lta > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta > > > > > > $Id: mri_robust_template.cpp,v 1.37.2.2 > 2012/10/10 > > 19:59:06 mreuter Exp $ > > > > --mov: Using > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > as > > movable/source volume. > > --mov: Using > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > as > > movable/source volume. > > Total: 2 input volumes > > --average: Using method 1 for template > computation. > > --template: Using > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > > as > > template output volume. > > --satit: Will estimate SAT iteratively! > > --inittp: Using TP 1 as target for > initialization > > --fixtp: Will map everything to init TP! > > --noit: Will output only first template (no > iterations)! > > --iscale: Enableing intensity scaling! > > --iscaleout: Will perform intensity scaling > and output results > > --subsample: Will subsample if size is > larger than 200 on > > all axes! > > --lta: Will output LTA transforms > > reading source > > > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... > > converting source > > > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' > > to > > bspline ... > > MRItoBSpline degree 3 > > reading source > > > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... > > converting source > > > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' > > to > > bspline ... > > MRItoBSpline degree 3 > > > > MultiRegistration::initializing Xforms (init > 1 , maxres 0 > > , iterate 5 , > > epsit 0.01 ) : > > > > [init] ========================= TP 2 to TP > 1 > > ============================== > > Register TP 2 ( > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > ) > > to TP 1 ( > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > ) > > > > -- Original : (0.4688, 0.4688, > 0.800001) mm size > > and (512, 512, 244) > > voxels. > > -- Resampled: (0.4688, 0.4688, > 0.4688) mm size and > > (512, 512, 417) > > voxels. > > -- Reslicing using cubic bspline > > MRItoBSpline degree 3 > > -- Original : (0.4688, 0.4688, > 0.800001) mm size > > and (512, 512, 244) > > voxels. > > -- Resampled: (0.4688, 0.4688, > 0.4688) mm size and > > (512, 512, 417) > > voxels. > > -- Reslicing using cubic bspline > > MRItoBSpline degree 3 > > > > - Max Resolution used: 3 > > -- gpS ( 64 , 64 , 52 ) > > -- gpT ( 64 , 64 , 52 ) > > - running loop to estimate saturation > parameter: > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Killed > > Linux localhost.localdomain > 2.6.32-504.el6.x86_64 #1 SMP > > Wed Oct 15 04:27:16 > > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > > > recon-all -s sub002 exited with ERRORS at > Thu Nov 5 > > 02:37:57 PST 2015 > > > > For more details, see the log file > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log > > To report a problem, see > > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > 2015-10-19 11:05 GMT+09:00 A-reum Min > <naniyaah(a)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(a)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(a)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(a)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(a)nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>>>: > > > > > > don't use "vertexno", just put > the > > vertex number, eg, > > --vox 33 0 0 > > > > > > > > > On 8/26/15 9:22 PM, A-reum Min > wrote: > > >> Hello developer, > > >> > > >> I have some question to you. > > >> > > >> How can i get the significant > vertices > > value using Qdec > > result? > > >> > > >> When i enter the 'mri_segstats > --i > > y.mgh --vox vertexno > > 33 0 0 > > >> --avgwf out.dat', then error > ouccured > > --> ERROR : > > Option out.dat > > >> unknown. > > >> > > >> So, i enter the 'mri_segstats > --i y.mgh > > --vox vertexno > > 33 0 0 > > >> --avgwf out.dat', then error > occured > > --> ERROR : Option > > 0 unkown. > > >> > > >> How can i fix it? > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> 2015-08-25 23:41 GMT+09:00 > Douglas > > Greve > > >> <greve(a)nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>>>: > > >> > > >> > > >> > > >> On 8/25/15 9:35 AM, A-reum > Min > > wrote: > > >>> Hello developers > > >>> > > >>> I have some question to > you. > > >>> > > >>> 1.In fig.png, how many > vertices > > were composed of > > cluster at > > >>> least? > > >> I'm not sure what you mean. > it does > > not look like > > there are > > >> any clusters there > > >>> > > >>> 2. How to change Area > > Threshold(fig.png)? > > >> The area is controlled by > the > > clusterwise threshold > > (--cwp) > > >> to mri_glmfit-sim > > >>> > > >>> 3. How to change CSD > > thresh(fig.png)? > > >> That is controlled by the > threshold > > when specifying > > "--cache > > >> threshold sign" to > mri_glmfit-sim > > >>> > > >>> 4. What is the difference > between > > two words(Area > > Threshold, > > >>> CSD thresh)? > > >> One is the cluster-pvalue > and the > > other is the > > >> cluster-forming thershold > > >>> > > >>> 5. What is the exactly > mean two > > words(Area > > Threshold, CSD > > >>> thresh)? > > >> See above > > >> > > >>> > > >>> Thank you > > >>> > > >>> 2015-08-12 23:23 GMT+09:00 > Douglas > > N Greve > > >>> <greve(a)nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>>>: > > >>> > > >>> > > >>> > > >>> On 08/10/2015 10:06 > PM, A-reum > > Min wrote: > > >>> > HI expert ! > > >>> > > > >>> > My name is Areum. I > have > > some question to > > you. > > >>> > > > >>> > 1. Does FreeSurfer > offer a > > effect size? if > > that offer, > > >>> how can i use > > >>> > effect size? > > >>> > > > >>> If you're doing a > group > > analysis, you can > > compute > > >>> fscalc > > glmdir/contrast/gamma.mgh div > > glmdir/rstd.mgh -o > > >>> glmdir/contrast/effectsize.mgh > > >>> > > > >>> > 2. I was wondering > about the > > stats.dat file > > in > > >>> stats_table (in Qdec > > >>> > folder). > > >>> > > > >>> > Stats.dat file’s > value mean > > that each area’s > > average > > >>> (include whole > > >>> > vertex) or each > > >>> > > > >>> > area’s average (only > > significant vertex)? > > >>> > > > >>> what stats.dat? if > > subject/stats/lh.aparc.stats, then > > >>> the area is the > > >>> total area for the ROI > > >>> > > > >>> > 3. Can I get whole > vertex > > value or > > significant vertex > > >>> value? Because, > > >>> > I want to > > >>> > > > >>> > compare two groups > > correlation using SPSS. In > > >>> addition, I want to > compare > > >>> > > > >>> > thickness, volume > and > > surface area > > correlation within > > >>> the one group > > >>> > using SPSS. > > >>> > > > >>> You can extract a > given vertex > > with > > >>> mri_segstats --i y.mgh --crs > > vertexno 0 0 > > --avgwf > > >>> vertexno.dat > > >>> vertexno.dat will be a text > > file with number of > > rows > > >>> equalt to thge > > >>> number of subjects > where the > > value is the data > > from the > > >>> given (0-based) > > >>> vertex no. y.mgh is > the input > > to mri_glmfit > > >>> > > > >>> > 4. I currently use > the > > default cluster > > >>> size(significant area > > threshold > > >>> > is 0mm^2). So, I > > >>> > > > >>> > want to control > cluster size > > larger than > > default > > >>> cluster size. How can > > >>> > I control the > > >>> > > > >>> > cluster size? > > >>> > > > >>> I don't know what you > mean. > > >>> > > > >>> > 5. In FreeSurfer > manual, GLM > > and Qdec have a > > same > > >>> results. But when I > > >>> > use the > > >>> > > > >>> > both(GLM, Qdec) > group > > analysis program > > results are not > > >>> same. What is > > >>> > differences > > >>> > > > >>> > between two analysis > > program? How can I get > > same > > >>> result while GLM and > > >>> > Qdec? > > >>> > > > >>> No way to know unless > you tell > > us the specifics > > of what > > >>> you did > > >>> > > > >>> > 6. How can I get > surface > > area and volume > > using > > >>> GLM(group analysis > > >>> > program)? > > >>> > > > >>> surface area and > volume are > > outputs of > > recon-all, not glm > > >>> > > > >>> > > > >>> > plz reply to me > > >>> > > > >>> > > > >>> > 2015-08-10 21:35 > GMT+09:00 > > A-reum Min > > >>> <naniyaah(a)gmail.com > > <mailto:naniyaah@gmail.com> > > <mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com>> > > >>> > <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com> > > <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>>>>: > > >>> > > > >>> > Hello developer~ > > >>> > > > >>> > I have some questions > to you. > > >>> > > > >>> > 1. Does FreeSurfer > offer a > > effect size? if that > > >>> offer, how can i > > >>> > use effect size? > > >>> > > > >>> > 2. I was wondering > about the > > stats.dat file in > > >>> stats_table (in > > >>> > Qdec folder). > > >>> > > > >>> > Stats.dat file’s value > mean > > that each area’s > > >>> average (include > > >>> > whole vertex) or each > > >>> > > > >>> > area’s average (only > > significant vertex)? > > >>> > > > >>> > 3. Can I get whole > vertex > > value or significant > > >>> vertex value? > > >>> > Because, I want to > > >>> > > > >>> > compare two groups > correlation > > using SPSS. In > > >>> addition, I want to > > >>> > compare > > >>> > > > >>> > thickness, volume and > surface > > area correlation > > >>> within the one > > >>> > group using SPSS. > > >>> > > > >>> > 4. I currently use the > default > > cluster > > >>> size(significant area > > >>> > threshold is 0mm^2). So, > I > > >>> > > > >>> > want to control > cluster size > > larger than > > default > > >>> cluster size. How > > >>> > can I control the > > >>> > > > >>> > cluster size? > > >>> > > > >>> > 5. In FreeSurfer > manual, GLM > > and Qdec have a > > same > > >>> results. But > > >>> > when I use the > > >>> > > > >>> > both(GLM, Qdec) group > analysis > > program results > > are > > >>> not same. What > > >>> > is differences > > >>> > > > >>> > between two analysis > program? > > How can I get > > same > > >>> result while GLM > > >>> > and Qdec? > > >>> > > > >>> > 6. How can I get > surface area > > and volume using > > >>> GLM(group analysis > > >>> > program)? > > >>> > > > >>> > > > >>> > thanks for your help > > >>> > > > >>> > > > >>> > 2015-07-27 14:28 > GMT+09:00 > > A-reum Min > > >>> <naniyaah(a)gmail.com > > <mailto:naniyaah@gmail.com> > > <mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com>> > > >>> > > <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com> > > >>> <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>>>>: > > >>> > > > >>> > Hello bruce > > >>> > > > >>> > I solve this > > problem(12.png) > > >>> > > > >>> > Thank you > > >>> > > > >>> > 2015-07-27 13:03 > GMT+09:00 > > dgw > > >>> <dgwakeman(a)gmail.com > > <mailto:dgwakeman@gmail.com> > > <mailto:dgwakeman@gmail.com > > <mailto:dgwakeman@gmail.com>> > > >>> > > > <mailto:dgwakeman@gmail.com > > <mailto:dgwakeman@gmail.com> > > >>> <mailto:dgwakeman@gmail.com > > <mailto:dgwakeman@gmail.com>>>>: > > >>> > > > >>> > Hi A-reum, > > >>> > > > >>> > I think you may be > > able to get a faster > > >>> response if you > > >>> > include some > > >>> > details about your > > setup: I would start > > >>> with the following: > > >>> > > > >>> > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > >>> > and run bugr. > > >>> > > > >>> > hth > > >>> > D > > >>> > > > >>> > On 7/26/15 5:17 PM, > > A-reum Min wrote: > > >>> > > Hi, Bruce > > >>> > > > > >>> > > When i use a Qdec, > > this > > message(12.png) > > >>> show up.. > > >>> > > How can i solve this > > problem? > > >>> > > > > >>> > > 2015-07-23 22:57 > > GMT+09:00 Bruce > > Fischl > > >>> > > > <fischl(a)nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>> > > >>> > > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>>> > > >>> > > > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>> > > >>> > > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>>>>>: > > >>> > > > > >>> > > 1. No, each > > subject has a > > different > > >>> #. You can map > > >>> > to fsaverage > > >>> > > (this is what > > -qcache does if you > > >>> specify it for > > >>> > recon-all), then > > >>> > > they will have > > the same #. > > >>> > > > > >>> > > 2. What result > > data do you mean? > > >>> > > > > >>> > > 3. Yes, although > > I'll leave the > > >>> details to Doug > > >>> > (since I don't > > >>> > > remember how his > > cluster code > > works). > > >>> > > > > >>> > > 4. The > > significance doesn't > > depend > > >>> on the cluster > > >>> > size unless you do > > >>> > > multiple comparison > > corrections (and > > >>> even then only > > >>> > if you do them a > > >>> > > certain way) > > >>> > > > > >>> > > cheers > > >>> > > Bruce > > >>> > > > > >>> > > > > >>> > > On Thu, 23 Jul > > 2015, A-reum Min > > wrote: > > >>> > > > > >>> > > HELLO developer > > >>> > > I have some > > question to you.. > > >>> > > > > >>> > > 1. Every > > patient is given to the > > >>> same number > > >>> > of vertex? > > >>> > > > > >>> > > 2. When i use a > > Qdec, How can I > > get the > > >>> > subject result data? > > >>> > > > > >>> > > 3. Could i get > > the significant > > vertex’s > > >>> > number, extent of the > > >>> > > significant area > > and gray matter > > volume? > > >>> > > > > >>> > > 4. Is it > > significant blue color > > >>> which how > > >>> > many connected > > >>> > > vertex? > > >>> > > > > >>> > > > > >>> > > 2015-05-29 2:03 > > GMT+09:00 A-reum Min > > >>> > <naniyaah(a)gmail.com > > <mailto:naniyaah@gmail.com> > > >>> <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>> > > <mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com> > > >>> <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>>> > > >>> > > > > <mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com> > > >>> <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>> > > >>> > > > <mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com> > > <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>>>>>: > > >>> > > hello developer~ > > >>> > > reconstruction is > > well done, so i'm > > >>> doing on > > >>> > 'qdec' step.. > > >>> > > Actually, i don't > > know how to treat > > the > > >>> Design > > >>> > menu exactly.. > > >>> > > > > >>> > > > >>> > > > -------------------------------------------------------------------------- > > - > > >>> > > Discrete(fixed > > factors) : diagnosis > > >>> > > continuous > > (covariate) : age , > > >>> > Left-Lateral-Ventricle > > >>> > > > > >>> > > > >>> > > > -------------------------------------------------------------------------- > > - > > >>> > > which one click > > before analyze? > > >>> > > > > >>> > > age range is > > 12years~24years/ > > >>> > > all subjects > > are adolescent. > > >>> > > and no > > outlier in age range.. > > >>> so.. age > > >>> > (continuous factor) > > does not > > >>> > > nasessart? > > >>> > > > > >>> > > > > >>> > > 2015-05-29 1:19 > > GMT+09:00 A-reum Min > > >>> > <naniyaah(a)gmail.com > > <mailto:naniyaah@gmail.com> > > >>> <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>> > > <mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com> > > >>> <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>>> > > >>> > > > > <mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com> > > >>> <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>> > > >>> > > > <mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com> > > <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>>>>>: > > >>> > > hello developer~ > > >>> > > reconstruction is > > well done, so i'm > > >>> doing on > > >>> > 'qdec' step.. > > >>> > > Actually, i don't > > know how to treat > > the > > >>> Design > > >>> > menu exactly.. > > >>> > > > > >>> > > > >>> > > > -------------------------------------------------------------------------- > > - > > >>> > > Discrete(fixed > > factors) : diagnosis > > >>> > > continuous > > (covariate) : age , > > >>> > Left-Lateral-Ventricle > > >>> > > > > >>> > > > >>> > > > -------------------------------------------------------------------------- > > - > > >>> > > which one click > > before analyze? > > >>> > > > > >>> > > > > >>> > > > > >>> > > 2015-04-05 21:41 > > GMT+09:00 Bruce > > Fischl > > >>> > > > > <fischl(a)nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>> > > >>> > > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>>> > > >>> > > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>> > > >>> > > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>>>>>: > > >>> > > I'm glad it worked > > out > > >>> > > Bruce > > >>> > > On Sun, 5 Apr > > 2015, A-reum Min > > wrote: > > >>> > > > > >>> > > Hello Bruce~ > > >>> > > You're > > right.. my PISA dicom > > file > > >>> > header > > >>> > > is too short > > >>> > > so, > > freesurfer didn't read > > it. > > >>> > > > > >>> > > Therefore I > > use another > > subjects > > >>> dicom > > >>> > > file and > > then freesurfer read > > it! > > >>> > > > > >>> > > thank you > > for u r adavice to > > me. > > >>> > > > > >>> > > I really > > appreciate u > > >>> > > > > >>> > > 2015-04-05 > > 7:08 GMT+09:00 > > Bruce > > >>> Fischl > > >>> > > > > <fischl(a)nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>> > > >>> > > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>>> > > >>> > > > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > >

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recon-all segmentation error
by Jaiashre Sridhar 27 Jan '16

27 Jan '16

Hello, We made changes to the aseg.mgz in the caudate, nucleus accumbens and ventricular region using Freeview. We are interested in getting the caudate volume. We used the following recon options in FreeSurfer v5.1.0: -autorecon2 -noaseg -autorecon3 Out of the 60 subjects that we ran, 4 exited with errors. I have provided the recon-all.log files. (1) Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations mhtVoxelList_Add(204, 160, 213, 229294): complete list too big! .. (2) CORRECTING DEFECT 6 (vertices=43037, convex hull=2066) Segmentation fault (3) mri_fill: could not find pons find_cutting_plane:seed point not in structure! Searching neighborhood.. (4) CORRECTING DEFECT 0 (vertices=96569, convex hull=3716) Excessive topologic defect encountered: could not allocate 980957071 edges for retessellation Cannot allocate memory Any help is greatly appreciated! Thanks, Jaiashre.

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Fwd: Call for Nominations: OHBM Young Investigator Award in Human Brain Mapping
by Douglas N Greve 27 Jan '16

27 Jan '16

-------- Forwarded Message -------- Subject: Call for Nominations: OHBM Young Investigator Award in Human Brain Mapping Date: Wed, 27 Jan 2016 12:05:27 -0600 From: info(a)humanbrainmapping.org Reply-To: info(a)humanbrainmapping.org To: greve(a)nmr.mgh.harvard.edu *Call for Nominations: OHBM Young Investigator Award in Human Brain Mapping (formerly Wiley Young Investigator Award)* The Organization for Human Brain Mapping, is pleased to announce the Call for Nominations for the OHBM Young Investigator Award in Human Brain Mapping. This award was formerly named the Wiley Young Investigator Award and will continue the tradition of recognizing a young investigator who has made significant contributions to the field of human brain mapping. The recipient will receive a cash award of $4,000 and an engraved plaque. Both are presented at the 22nd OHBM Annual Meeting being held on June 26-30, 2016 in Geneva, Switzerland. For additional Annual Meeting information, please visit our website. <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=33…> Each nomination should be no more than two pages and must include the following: 1. A brief statement giving the reasons for nomination and commenting on the nominee's contributions to the field of human brain mapping; 2. A short biographical statement on the nominee, including: Name; Date of birth; Present affiliation; Current mailing address; Current phone, fax and email; Advance professional degrees (including institutions and dates); List of postdoctoral fellowships, residencies and professional appointments (including dates of service); 3. A short list of *most notable* publications; URL of website (if available) Nominations may be made by any individual other than the nominee. To be eligible for this award, nominees are required to: 1. Be under 40 years of age on July 1, 2016 2. Be within 10 years of completing postdoctoral fellowship or residency on July 1, 2016; 3. Have made significant contributions to the field of human brain mapping. Please send nominations by March 18th, 2016, 12:00 PM US Central Standard time to: info(a)humanbrainmapping.org. <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=33….> Nominations will be evaluated with final selections made by the OHBM Council. The recipient of the award will be notified by April 15, 2016. View a list of past Wiley Young Investigator Award Recipients. <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=33…> ------------------------------------------------------------------------ Organization for Human Brain Mapping (OHBM) 5841 Cedar Lake Road, Suite 204 Minneapolis, MN 55416 USA info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=33…> www.humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=33…> To opt out of OHBM emails, contact the OHBM Executive Office at info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=33…>. Call Send SMS Add to Skype You'll need Skype CreditFree via Skype Click here to Unsubscribe <http://www.humanbrainmapping.org/i4a/etrack/unsub.cfm?campaignID=3382&conta…>

1 0

Ref FAST and results visualization issue
by stdp82＠virgilio.it 27 Jan '16

27 Jan '16

Hi list, I have two requests please. A- I need to have a reference for FS-FAST (seed based analysis on rs data) B- I have difficulties for results visualization. How can I do to visualize the the cortical areas which are functionally connected with the controlateral seed? For example, my seed are right and left amygdala.To visualize RIGHT amygdala - RIGHT cortex connectivity I'm doing: cd my-group/fc.ramgseed.surf.lh/R_Amygdala tksurfer fsaverage rh inflated -aparc -overlay my-glm.wls/intercept/sig.nii.gz and all is fine. To visualize RIGHT amygdala - LEFT cortex connectivity I'm doing: tksurfer fsaverage lh inflated -aparc -overlay my-glm.wls/intercept/sig.nii.gz but the image is so confused. It seem to be the translated image which I have projected in the right semi. Thanks Stefano

1 0

Re: [Freesurfer] FreeSurfer Lateral Ventricles Error
by Allison Leigh Rainford 27 Jan '16

27 Jan '16

Attached are screenshots of the initial issue and the issue after my attempt to correct it. [cid:CB5F258E-AFA1-430D-B7E6-167D5A5FE966][cid:8F112E13-A56B-4C1B-9310-15436F1F4FF4]

1 0

Postdoctoral Fellow at Emory University
by Junjie Wu 27 Jan '16

27 Jan '16

The Departments of Medicine and of Radiology and Imaging Sciences at Emory University is seeking a postdoctoral fellow to work with a team of physicians and neuroscientists focused on neuroimaging (MRI: Arterial Spin Labeling and cerebrovascular reactivity). The position provides excellent opportunity to work in an interdisciplinary environment and have close interactions with MR physicists, radiologists, neurologist, internists and neuroscientists. Accesses are available to two dedicated research MR 3T Siemens Tim-Trio scanners, one 9.4T animal scanner, and a powerful computer-cluster. Close collaboration with the Emory University Hospital, which houses a clinical 3T Siemens Tim-Trio and five 1.5T MR scanners, allows easy translation of technical developments to clinical settings. The qualifications of a successful candidate should include · A PhD degree in Electrical Engineering, Biomedical Engineering, Physics, or other related fields · Strong background in signal processing, image processing and quantitative analysis. Excellent proficiency with Matlab and/or C/C++ programming language. · Demonstrated independent research capabilities and good organizational and inter-personal skills. Previous experiences with medical image processing including freesrufer, FSL and SPM are desirable; The candidate is expected to work on projects involving performing image processing using existing tools and development of new methodologies. Potential research projects depend on the mutual interests of the candidate and the PI. These may include but are not limited to: (1) analyzing CO2-vasoreactivity images; (2) reconstruction and analysis methods for quantitative susceptibility mapping (QSM), (3) quantification and analysis methods for arterial spin labeling, dynamic susceptibility contrast imaging and diffusion imaging. Plans to obtain independent funding is highly desirable. Emory University provides competitive salaries commensurate with experience. This position is funded by NIH grants for at least 5 years. To apply, please send your CV to Ihab Hajjar, MD (ihajjar(a)emory.edu) and Deqiang Qiu, PhD (dqiu3(a)emory.edu)

1 0

tracula quality assessment dwi_motion.txt units
by Ruth Carper 27 Jan '16

27 Jan '16

What are the units of measure for translation and rotation as output in the dwi_motion.txt file from Tracula? It's not stated in the output file or on the page http://freesurfer.net/fswiki/FsTutorial/TraculaOutputsI would have assumed mm and degrees, but the rotation values are consistently less than 0.01, which doesn't seem likely. --Ruth

2 1

FreeSurfer Lateral Ventricles Error
by Allison Leigh Rainford 27 Jan '16

27 Jan '16

?Good morning, I am editing a brain using FreeSurfer version 5.1 and I have a pial and white matter boundary issue that persists in the lateral ventricles, specifically where the software would draw a boundary between the right and left hemispheres of the brain. Upon running it through the recon-all pipeline, it reconstructed those ventricle boundaries in a way that the boundaries did not even touch the walls of the ventricles and had the boundary lines cutting through the middle of the left and right lateral ventricles. After fully filling the ventricles with 255's on the wm.mgz file (to match the general reconstruction of other brains we have worked on), the issue still largely persists. The pial and white matter boundaries now more accurately follow the outer edges of the ventricles but the boundaries that separate the left and right hemisphere are still very messy. This issue can be found in over 60 slices throughout the brain. Any and all help is appreciated. Best, Allison

1 1

Statistical analyses with QDEC
by Francesco Cardinale 27 Jan '16

27 Jan '16

Dear Freesurfer experts, I have some questions about statistical analyses. How to adjust for sex and age? I use the precompiled Freesurfer 5.3.0 MacOSX version, and its tool QDEC to compare cortical thickness between two groups. I would like to use age and sex as nuisance factors. No problem with the age, but I don’t see the sex in the list of usable variables if I code it as a categorical variable (male / female). On the opposite, If I code it as numbers (male = 1, female = 2) I can use it, but how can I declare that it is a factor and not a continuous numerical variable? I don’t want that “female” affects the fitting of the GLM with a value that means “male” * 2. What about the use of other morphometric properties as nuisance factors? For example, how could I use sulcality or LGI as nuisance factors? Is it possible to use more than one scalar simultaneously? Similarly to question 2, is it possible to use home-made *.mgh scalars as a nuisance factors? How? Do the command-line tools allow such analyses better than QDEC? Related to my questions, which features do they add? In this field of interest, are there any major advantages coming with Freesurfer 6.0? Thanks a lot and best regards Cico Francesco Cardinale, MD Neurosurgeon "Claudio Munari" Centre for Epilepsy and Parkinson Surgery - Ospedale Niguarda "Ca' Granda" Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia <x-apple-data-detectors://0/0> phone 0039 02 64442917 <tel:0039%2002%2064442917> fax 0039 02 64442868 <tel:0039%2002%2064442868> e-mail francesco.cardinale(a)ospedaleniguarda.it <mailto:francesco.cardinale@ospedaleniguarda.it>

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Re: [Freesurfer] Reg: CORRECTING DEFECT 126 (vertices=61161, convex hull=14255)
by Bruce Fischl 27 Jan '16

27 Jan '16

Hi Jesu can you please post this type of question to the FS list so others can reply and/or learn from the answer? This defect is too big - the defect correction grows quadratically in time with the number of vertices in the defect. vertices=61161 means that you have a defect that is about half the size of the total surface. You need to look at the ?h.orig.nofix and/or the ?h.inflated.nofix and figure out what the defect is and correct it by either editing the wm.mgz or adding control points. If you can't figure this out you can upload the entire subject dir to our ftp site and one of us will take a look. cheers Bruce On Wed, 27 Jan 2016, Jesu Kiran Spurgen wrote: > Dear Prof. Fischl, > Good Afternoon! I have been running freesurfer for a patient data, and have > to find this retesselalation of defect. I have successful with some data but > for some others it looks frozen even after 4 days. Could you please kindly > suggest what I could do here? How could I get some results overriding this > particular step? > > I would extremely grateful for your kind reply and help. > > Warm regards, > > > Jesu Kiran Spurgen > Postgraduate Student, Advanced Medical Imaging > KU Leuven, Belgium > >

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