Can you send the contents of glm_double_all_ps_0/analysis.info ?
Apologies for delayed response--here is the full terminal output. (error in bold)
--------------------------------------------------------------
selxavg3-sess logfile is /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm/log/selxavg3-sess-bold-glm_double_all_ps_0-170417150715.log
--------------------------------------------------------------
preproc-sess -s 170322_xu_binding01_sub01 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog
--------------------------------------------------------------
preproc-sess logfile is /dev/null
--------------------------------------------------------------
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
jtaylor
setenv FREESURFER_HOME /ncf/nrg/sw/apps/freesurfer/5.3.0
setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
/ncf/vcn/jtaylor/programs/batch_edits/preproc-sess
-s 170322_xu_binding01_sub01 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog
Mon Apr 17 15:07:18 EDT 2017
instem f
mc 1 f fmc
stc 0 fmc
sm 0 fmc
mask 1 brain
170322_xu_binding01_sub01 Template -----------------------------
mktemplate-sess -s 170322_xu_binding01_sub01 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -nolog -update
Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01 ----------------
Mon Apr 17 15:07:18 EDT 2017
Detected input format at nii.gz
170322_xu_binding01_sub01 Update not needed
Run: 008 ----------------
Mon Apr 17 15:07:19 EDT 2017
170322_xu_binding01_sub01 008 Update not needed
Run: 010 ----------------
Mon Apr 17 15:07:19 EDT 2017
170322_xu_binding01_sub01 010 Update not needed
Run: 012 ----------------
Mon Apr 17 15:07:19 EDT 2017
170322_xu_binding01_sub01 012 Update not needed
Run: 020 ----------------
Mon Apr 17 15:07:19 EDT 2017
170322_xu_binding01_sub01 020 Update not needed
Run: 022 ----------------
Mon Apr 17 15:07:19 EDT 2017
170322_xu_binding01_sub01 022 Update not needed
Run: 024 ----------------
Mon Apr 17 15:07:19 EDT 2017
170322_xu_binding01_sub01 024 Update not needed
Run: 034 ----------------
Mon Apr 17 15:07:19 EDT 2017
170322_xu_binding01_sub01 034 Update not needed
Run: 036 ----------------
Mon Apr 17 15:07:19 EDT 2017
170322_xu_binding01_sub01 036 Update not needed
Run: 038 ----------------
Mon Apr 17 15:07:19 EDT 2017
170322_xu_binding01_sub01 038 Update not needed
Run: 046 ----------------
Mon Apr 17 15:07:19 EDT 2017
170322_xu_binding01_sub01 046 Update not needed
Run: 048 ----------------
Mon Apr 17 15:07:19 EDT 2017
170322_xu_binding01_sub01 048 Update not needed
Run: 050 ----------------
Mon Apr 17 15:07:19 EDT 2017
170322_xu_binding01_sub01 050 Update not needed
Mon Apr 17 15:07:19 EDT 2017
mktemplate-sess completed
170322_xu_binding01_sub01 Mask ------------------------
mkbrainmask-sess -maskstem brain -fsd bold -s 170322_xu_binding01_sub01 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -rlf runlist_double.txt -nolog -update
------------------------------------------------
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01
Mon Apr 17 15:07:19 EDT 2017
170322_xu_binding01_sub01 Update not needed for session-level mask
170322_xu_binding01_sub01 Update not needed for run 008 mask
170322_xu_binding01_sub01 Update not needed for run 008 meanval
170322_xu_binding01_sub01 Update not needed for run 010 mask
170322_xu_binding01_sub01 Update not needed for run 010 meanval
170322_xu_binding01_sub01 Update not needed for run 012 mask
170322_xu_binding01_sub01 Update not needed for run 012 meanval
170322_xu_binding01_sub01 Update not needed for run 020 mask
170322_xu_binding01_sub01 Update not needed for run 020 meanval
170322_xu_binding01_sub01 Update not needed for run 022 mask
170322_xu_binding01_sub01 Update not needed for run 022 meanval
170322_xu_binding01_sub01 Update not needed for run 024 mask
170322_xu_binding01_sub01 Update not needed for run 024 meanval
170322_xu_binding01_sub01 Update not needed for run 034 mask
170322_xu_binding01_sub01 Update not needed for run 034 meanval
170322_xu_binding01_sub01 Update not needed for run 036 mask
170322_xu_binding01_sub01 Update not needed for run 036 meanval
170322_xu_binding01_sub01 Update not needed for run 038 mask
170322_xu_binding01_sub01 Update not needed for run 038 meanval
170322_xu_binding01_sub01 Update not needed for run 046 mask
170322_xu_binding01_sub01 Update not needed for run 046 meanval
170322_xu_binding01_sub01 Update not needed for run 048 mask
170322_xu_binding01_sub01 Update not needed for run 048 meanval
170322_xu_binding01_sub01 Update not needed for run 050 mask
170322_xu_binding01_sub01 Update not needed for run 050 meanval
Mon Apr 17 15:07:21 EDT 2017
mkbrainmask-sess done
170322_xu_binding01_sub01 Registration -----------------------------
register-sess -s 170322_xu_binding01_sub01 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
--------------------------------------------------------------
register-sess logfile is /dev/null
--------------------------------------------------------------
Mon Apr 17 15:07:22 EDT 2017
setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
cd /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
/ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/register-sess -s 170322_xu_binding01_sub01 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01 ----------------
Mon Apr 17 15:07:22 EDT 2017
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01
Mon Apr 17 15:07:22 EDT 2017
register-sess completed
170322_xu_binding01_sub01 MC -----------------------------
mc-sess -fstem f -fmcstem fmc -s 170322_xu_binding01_sub01 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -per-session -nolog -update
Logfile is /dev/null
-------------------------------------------
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01
RunList: 008 010 012 020 022 024 034 036 038 046 048 050
170322_xu_binding01_sub01 008 Update not needed
170322_xu_binding01_sub01 010 Update not needed
170322_xu_binding01_sub01 012 Update not needed
170322_xu_binding01_sub01 020 Update not needed
170322_xu_binding01_sub01 022 Update not needed
170322_xu_binding01_sub01 024 Update not needed
170322_xu_binding01_sub01 034 Update not needed
170322_xu_binding01_sub01 036 Update not needed
170322_xu_binding01_sub01 038 Update not needed
170322_xu_binding01_sub01 046 Update not needed
170322_xu_binding01_sub01 048 Update not needed
170322_xu_binding01_sub01 050 Update not needed
Mon Apr 17 15:07:22 EDT 2017
mc-sess completed SUCCESSFULLY
----------------------------------------
Started at Mon Apr 17 15:07:18 EDT 2017
Ended at Mon Apr 17 15:07:22 EDT 2017
preproc-sess done
preproc-sess -s 170329_xu_binding01_sub02 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog
--------------------------------------------------------------
preproc-sess logfile is /dev/null
--------------------------------------------------------------
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
jtaylor
setenv FREESURFER_HOME /ncf/nrg/sw/apps/freesurfer/5.3.0
setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
/ncf/vcn/jtaylor/programs/batch_edits/preproc-sess
-s 170329_xu_binding01_sub02 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog
Mon Apr 17 15:07:23 EDT 2017
instem f
mc 1 f fmc
stc 0 fmc
sm 0 fmc
mask 1 brain
170329_xu_binding01_sub02 Template -----------------------------
mktemplate-sess -s 170329_xu_binding01_sub02 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -nolog -update
Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170329_xu_binding01_sub02 ----------------
Mon Apr 17 15:07:23 EDT 2017
Detected input format at nii.gz
170329_xu_binding01_sub02 Update not needed
Run: 014 ----------------
Mon Apr 17 15:07:23 EDT 2017
170329_xu_binding01_sub02 014 Update not needed
Run: 016 ----------------
Mon Apr 17 15:07:23 EDT 2017
170329_xu_binding01_sub02 016 Update not needed
Run: 018 ----------------
Mon Apr 17 15:07:23 EDT 2017
170329_xu_binding01_sub02 018 Update not needed
Run: 026 ----------------
Mon Apr 17 15:07:23 EDT 2017
170329_xu_binding01_sub02 026 Update not needed
Run: 028 ----------------
Mon Apr 17 15:07:23 EDT 2017
170329_xu_binding01_sub02 028 Update not needed
Run: 030 ----------------
Mon Apr 17 15:07:24 EDT 2017
170329_xu_binding01_sub02 030 Update not needed
Run: 040 ----------------
Mon Apr 17 15:07:24 EDT 2017
170329_xu_binding01_sub02 040 Update not needed
Run: 042 ----------------
Mon Apr 17 15:07:24 EDT 2017
170329_xu_binding01_sub02 042 Update not needed
Run: 044 ----------------
Mon Apr 17 15:07:24 EDT 2017
170329_xu_binding01_sub02 044 Update not needed
Run: 052 ----------------
Mon Apr 17 15:07:24 EDT 2017
170329_xu_binding01_sub02 052 Update not needed
Run: 054 ----------------
Mon Apr 17 15:07:24 EDT 2017
170329_xu_binding01_sub02 054 Update not needed
Run: 056 ----------------
Mon Apr 17 15:07:24 EDT 2017
170329_xu_binding01_sub02 056 Update not needed
Mon Apr 17 15:07:24 EDT 2017
mktemplate-sess completed
170329_xu_binding01_sub02 Mask ------------------------
mkbrainmask-sess -maskstem brain -fsd bold -s 170329_xu_binding01_sub02 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -rlf runlist_double.txt -nolog -update
------------------------------------------------
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170329_xu_binding01_sub02
Mon Apr 17 15:07:24 EDT 2017
170329_xu_binding01_sub02 Update not needed for session-level mask
170329_xu_binding01_sub02 Update not needed for run 014 mask
170329_xu_binding01_sub02 Update not needed for run 014 meanval
170329_xu_binding01_sub02 Update not needed for run 016 mask
170329_xu_binding01_sub02 Update not needed for run 016 meanval
170329_xu_binding01_sub02 Update not needed for run 018 mask
170329_xu_binding01_sub02 Update not needed for run 018 meanval
170329_xu_binding01_sub02 Update not needed for run 026 mask
170329_xu_binding01_sub02 Update not needed for run 026 meanval
170329_xu_binding01_sub02 Update not needed for run 028 mask
170329_xu_binding01_sub02 Update not needed for run 028 meanval
170329_xu_binding01_sub02 Update not needed for run 030 mask
170329_xu_binding01_sub02 Update not needed for run 030 meanval
170329_xu_binding01_sub02 Update not needed for run 040 mask
170329_xu_binding01_sub02 Update not needed for run 040 meanval
170329_xu_binding01_sub02 Update not needed for run 042 mask
170329_xu_binding01_sub02 Update not needed for run 042 meanval
170329_xu_binding01_sub02 Update not needed for run 044 mask
170329_xu_binding01_sub02 Update not needed for run 044 meanval
170329_xu_binding01_sub02 Update not needed for run 052 mask
170329_xu_binding01_sub02 Update not needed for run 052 meanval
170329_xu_binding01_sub02 Update not needed for run 054 mask
170329_xu_binding01_sub02 Update not needed for run 054 meanval
170329_xu_binding01_sub02 Update not needed for run 056 mask
170329_xu_binding01_sub02 Update not needed for run 056 meanval
Mon Apr 17 15:07:27 EDT 2017
mkbrainmask-sess done
170329_xu_binding01_sub02 Registration -----------------------------
register-sess -s 170329_xu_binding01_sub02 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
--------------------------------------------------------------
register-sess logfile is /dev/null
--------------------------------------------------------------
Mon Apr 17 15:07:27 EDT 2017
setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
cd /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
/ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/register-sess -s 170329_xu_binding01_sub02 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170329_xu_binding01_sub02 ----------------
Mon Apr 17 15:07:27 EDT 2017
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170329_xu_binding01_sub02
Mon Apr 17 15:07:27 EDT 2017
register-sess completed
170329_xu_binding01_sub02 MC -----------------------------
mc-sess -fstem f -fmcstem fmc -s 170329_xu_binding01_sub02 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -per-session -nolog -update
Logfile is /dev/null
-------------------------------------------
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170329_xu_binding01_sub02
RunList: 014 016 018 026 028 030 040 042 044 052 054 056
170329_xu_binding01_sub02 014 Update not needed
170329_xu_binding01_sub02 016 Update not needed
170329_xu_binding01_sub02 018 Update not needed
170329_xu_binding01_sub02 026 Update not needed
170329_xu_binding01_sub02 028 Update not needed
170329_xu_binding01_sub02 030 Update not needed
170329_xu_binding01_sub02 040 Update not needed
170329_xu_binding01_sub02 042 Update not needed
170329_xu_binding01_sub02 044 Update not needed
170329_xu_binding01_sub02 052 Update not needed
170329_xu_binding01_sub02 054 Update not needed
170329_xu_binding01_sub02 056 Update not needed
Mon Apr 17 15:07:28 EDT 2017
mc-sess completed SUCCESSFULLY
----------------------------------------
Started at Mon Apr 17 15:07:23 EDT 2017
Ended at Mon Apr 17 15:07:28 EDT 2017
preproc-sess done
preproc-sess -s 170402_xu_binding01_sub03 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog
--------------------------------------------------------------
preproc-sess logfile is /dev/null
--------------------------------------------------------------
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
jtaylor
setenv FREESURFER_HOME /ncf/nrg/sw/apps/freesurfer/5.3.0
setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
/ncf/vcn/jtaylor/programs/batch_edits/preproc-sess
-s 170402_xu_binding01_sub03 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog
Mon Apr 17 15:07:28 EDT 2017
instem f
mc 1 f fmc
stc 0 fmc
sm 0 fmc
mask 1 brain
170402_xu_binding01_sub03 Template -----------------------------
mktemplate-sess -s 170402_xu_binding01_sub03 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -nolog -update
Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub03 ----------------
Mon Apr 17 15:07:29 EDT 2017
Detected input format at nii.gz
170402_xu_binding01_sub03 Update not needed
Run: 008 ----------------
Mon Apr 17 15:07:29 EDT 2017
170402_xu_binding01_sub03 008 Update not needed
Run: 010 ----------------
Mon Apr 17 15:07:29 EDT 2017
170402_xu_binding01_sub03 010 Update not needed
Run: 012 ----------------
Mon Apr 17 15:07:29 EDT 2017
170402_xu_binding01_sub03 012 Update not needed
Run: 020 ----------------
Mon Apr 17 15:07:29 EDT 2017
170402_xu_binding01_sub03 020 Update not needed
Run: 022 ----------------
Mon Apr 17 15:07:29 EDT 2017
170402_xu_binding01_sub03 022 Update not needed
Run: 024 ----------------
Mon Apr 17 15:07:29 EDT 2017
170402_xu_binding01_sub03 024 Update not needed
Run: 034 ----------------
Mon Apr 17 15:07:29 EDT 2017
170402_xu_binding01_sub03 034 Update not needed
Run: 036 ----------------
Mon Apr 17 15:07:29 EDT 2017
170402_xu_binding01_sub03 036 Update not needed
Run: 038 ----------------
Mon Apr 17 15:07:29 EDT 2017
170402_xu_binding01_sub03 038 Update not needed
Run: 046 ----------------
Mon Apr 17 15:07:29 EDT 2017
170402_xu_binding01_sub03 046 Update not needed
Run: 048 ----------------
Mon Apr 17 15:07:29 EDT 2017
170402_xu_binding01_sub03 048 Update not needed
Run: 050 ----------------
Mon Apr 17 15:07:29 EDT 2017
170402_xu_binding01_sub03 050 Update not needed
Mon Apr 17 15:07:29 EDT 2017
mktemplate-sess completed
170402_xu_binding01_sub03 Mask ------------------------
mkbrainmask-sess -maskstem brain -fsd bold -s 170402_xu_binding01_sub03 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -rlf runlist_double.txt -nolog -update
------------------------------------------------
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub03
Mon Apr 17 15:07:29 EDT 2017
170402_xu_binding01_sub03 Update not needed for session-level mask
170402_xu_binding01_sub03 Update not needed for run 008 mask
170402_xu_binding01_sub03 Update not needed for run 008 meanval
170402_xu_binding01_sub03 Update not needed for run 010 mask
170402_xu_binding01_sub03 Update not needed for run 010 meanval
170402_xu_binding01_sub03 Update not needed for run 012 mask
170402_xu_binding01_sub03 Update not needed for run 012 meanval
170402_xu_binding01_sub03 Update not needed for run 020 mask
170402_xu_binding01_sub03 Update not needed for run 020 meanval
170402_xu_binding01_sub03 Update not needed for run 022 mask
170402_xu_binding01_sub03 Update not needed for run 022 meanval
170402_xu_binding01_sub03 Update not needed for run 024 mask
170402_xu_binding01_sub03 Update not needed for run 024 meanval
170402_xu_binding01_sub03 Update not needed for run 034 mask
170402_xu_binding01_sub03 Update not needed for run 034 meanval
170402_xu_binding01_sub03 Update not needed for run 036 mask
170402_xu_binding01_sub03 Update not needed for run 036 meanval
170402_xu_binding01_sub03 Update not needed for run 038 mask
170402_xu_binding01_sub03 Update not needed for run 038 meanval
170402_xu_binding01_sub03 Update not needed for run 046 mask
170402_xu_binding01_sub03 Update not needed for run 046 meanval
170402_xu_binding01_sub03 Update not needed for run 048 mask
170402_xu_binding01_sub03 Update not needed for run 048 meanval
170402_xu_binding01_sub03 Update not needed for run 050 mask
170402_xu_binding01_sub03 Update not needed for run 050 meanval
Mon Apr 17 15:07:32 EDT 2017
mkbrainmask-sess done
170402_xu_binding01_sub03 Registration -----------------------------
register-sess -s 170402_xu_binding01_sub03 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
--------------------------------------------------------------
register-sess logfile is /dev/null
--------------------------------------------------------------
Mon Apr 17 15:07:32 EDT 2017
setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
cd /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
/ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/register-sess -s 170402_xu_binding01_sub03 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub03 ----------------
Mon Apr 17 15:07:32 EDT 2017
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub03
Mon Apr 17 15:07:32 EDT 2017
register-sess completed
170402_xu_binding01_sub03 MC -----------------------------
mc-sess -fstem f -fmcstem fmc -s 170402_xu_binding01_sub03 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -per-session -nolog -update
Logfile is /dev/null
-------------------------------------------
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub03
RunList: 008 010 012 020 022 024 034 036 038 046 048 050
170402_xu_binding01_sub03 008 Update not needed
170402_xu_binding01_sub03 010 Update not needed
170402_xu_binding01_sub03 012 Update not needed
170402_xu_binding01_sub03 020 Update not needed
170402_xu_binding01_sub03 022 Update not needed
170402_xu_binding01_sub03 024 Update not needed
170402_xu_binding01_sub03 034 Update not needed
170402_xu_binding01_sub03 036 Update not needed
170402_xu_binding01_sub03 038 Update not needed
170402_xu_binding01_sub03 046 Update not needed
170402_xu_binding01_sub03 048 Update not needed
170402_xu_binding01_sub03 050 Update not needed
Mon Apr 17 15:07:33 EDT 2017
mc-sess completed SUCCESSFULLY
----------------------------------------
Started at Mon Apr 17 15:07:28 EDT 2017
Ended at Mon Apr 17 15:07:33 EDT 2017
preproc-sess done
preproc-sess -s 170402_xu_binding01_sub04 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog
--------------------------------------------------------------
preproc-sess logfile is /dev/null
--------------------------------------------------------------
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
jtaylor
setenv FREESURFER_HOME /ncf/nrg/sw/apps/freesurfer/5.3.0
setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
/ncf/vcn/jtaylor/programs/batch_edits/preproc-sess
-s 170402_xu_binding01_sub04 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog
Mon Apr 17 15:07:33 EDT 2017
instem f
mc 1 f fmc
stc 0 fmc
sm 0 fmc
mask 1 brain
170402_xu_binding01_sub04 Template -----------------------------
mktemplate-sess -s 170402_xu_binding01_sub04 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -nolog -update
Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub04 ----------------
Mon Apr 17 15:07:33 EDT 2017
Detected input format at nii.gz
170402_xu_binding01_sub04 Update not needed
Run: 014 ----------------
Mon Apr 17 15:07:34 EDT 2017
170402_xu_binding01_sub04 014 Update not needed
Run: 016 ----------------
Mon Apr 17 15:07:34 EDT 2017
170402_xu_binding01_sub04 016 Update not needed
Run: 018 ----------------
Mon Apr 17 15:07:34 EDT 2017
170402_xu_binding01_sub04 018 Update not needed
Run: 026 ----------------
Mon Apr 17 15:07:34 EDT 2017
170402_xu_binding01_sub04 026 Update not needed
Run: 028 ----------------
Mon Apr 17 15:07:34 EDT 2017
170402_xu_binding01_sub04 028 Update not needed
Run: 030 ----------------
Mon Apr 17 15:07:34 EDT 2017
170402_xu_binding01_sub04 030 Update not needed
Run: 040 ----------------
Mon Apr 17 15:07:34 EDT 2017
170402_xu_binding01_sub04 040 Update not needed
Run: 042 ----------------
Mon Apr 17 15:07:34 EDT 2017
170402_xu_binding01_sub04 042 Update not needed
Run: 044 ----------------
Mon Apr 17 15:07:34 EDT 2017
170402_xu_binding01_sub04 044 Update not needed
Run: 052 ----------------
Mon Apr 17 15:07:34 EDT 2017
170402_xu_binding01_sub04 052 Update not needed
Run: 054 ----------------
Mon Apr 17 15:07:34 EDT 2017
170402_xu_binding01_sub04 054 Update not needed
Run: 056 ----------------
Mon Apr 17 15:07:34 EDT 2017
170402_xu_binding01_sub04 056 Update not needed
Mon Apr 17 15:07:34 EDT 2017
mktemplate-sess completed
170402_xu_binding01_sub04 Mask ------------------------
mkbrainmask-sess -maskstem brain -fsd bold -s 170402_xu_binding01_sub04 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -rlf runlist_double.txt -nolog -update
------------------------------------------------
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub04
Mon Apr 17 15:07:34 EDT 2017
170402_xu_binding01_sub04 Update not needed for session-level mask
170402_xu_binding01_sub04 Update not needed for run 014 mask
170402_xu_binding01_sub04 Update not needed for run 014 meanval
170402_xu_binding01_sub04 Update not needed for run 016 mask
170402_xu_binding01_sub04 Update not needed for run 016 meanval
170402_xu_binding01_sub04 Update not needed for run 018 mask
170402_xu_binding01_sub04 Update not needed for run 018 meanval
170402_xu_binding01_sub04 Update not needed for run 026 mask
170402_xu_binding01_sub04 Update not needed for run 026 meanval
170402_xu_binding01_sub04 Update not needed for run 028 mask
170402_xu_binding01_sub04 Update not needed for run 028 meanval
170402_xu_binding01_sub04 Update not needed for run 030 mask
170402_xu_binding01_sub04 Update not needed for run 030 meanval
170402_xu_binding01_sub04 Update not needed for run 040 mask
170402_xu_binding01_sub04 Update not needed for run 040 meanval
170402_xu_binding01_sub04 Update not needed for run 042 mask
170402_xu_binding01_sub04 Update not needed for run 042 meanval
170402_xu_binding01_sub04 Update not needed for run 044 mask
170402_xu_binding01_sub04 Update not needed for run 044 meanval
170402_xu_binding01_sub04 Update not needed for run 052 mask
170402_xu_binding01_sub04 Update not needed for run 052 meanval
170402_xu_binding01_sub04 Update not needed for run 054 mask
170402_xu_binding01_sub04 Update not needed for run 054 meanval
170402_xu_binding01_sub04 Update not needed for run 056 mask
170402_xu_binding01_sub04 Update not needed for run 056 meanval
Mon Apr 17 15:07:36 EDT 2017
mkbrainmask-sess done
170402_xu_binding01_sub04 Registration -----------------------------
register-sess -s 170402_xu_binding01_sub04 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
--------------------------------------------------------------
register-sess logfile is /dev/null
--------------------------------------------------------------
Mon Apr 17 15:07:37 EDT 2017
setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
cd /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
/ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/register-sess -s 170402_xu_binding01_sub04 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub04 ----------------
Mon Apr 17 15:07:37 EDT 2017
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub04
Mon Apr 17 15:07:37 EDT 2017
register-sess completed
170402_xu_binding01_sub04 MC -----------------------------
mc-sess -fstem f -fmcstem fmc -s 170402_xu_binding01_sub04 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -per-session -nolog -update
Logfile is /dev/null
-------------------------------------------
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub04
RunList: 014 016 018 026 028 030 040 042 044 052 054 056
170402_xu_binding01_sub04 014 Update not needed
170402_xu_binding01_sub04 016 Update not needed
170402_xu_binding01_sub04 018 Update not needed
170402_xu_binding01_sub04 026 Update not needed
170402_xu_binding01_sub04 028 Update not needed
170402_xu_binding01_sub04 030 Update not needed
170402_xu_binding01_sub04 040 Update not needed
170402_xu_binding01_sub04 042 Update not needed
170402_xu_binding01_sub04 044 Update not needed
170402_xu_binding01_sub04 052 Update not needed
170402_xu_binding01_sub04 054 Update not needed
170402_xu_binding01_sub04 056 Update not needed
Mon Apr 17 15:07:37 EDT 2017
mc-sess completed SUCCESSFULLY
----------------------------------------
Started at Mon Apr 17 15:07:33 EDT 2017
Ended at Mon Apr 17 15:07:37 EDT 2017
preproc-sess done
preproc-sess -s 170412_xu_binding01_sub05 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog
--------------------------------------------------------------
preproc-sess logfile is /dev/null
--------------------------------------------------------------
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
jtaylor
setenv FREESURFER_HOME /ncf/nrg/sw/apps/freesurfer/5.3.0
setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
/ncf/vcn/jtaylor/programs/batch_edits/preproc-sess
-s 170412_xu_binding01_sub05 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog
Mon Apr 17 15:07:38 EDT 2017
instem f
mc 1 f fmc
stc 0 fmc
sm 0 fmc
mask 1 brain
170412_xu_binding01_sub05 Template -----------------------------
mktemplate-sess -s 170412_xu_binding01_sub05 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -nolog -update
Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170412_xu_binding01_sub05 ----------------
Mon Apr 17 15:07:38 EDT 2017
Detected input format at nii.gz
170412_xu_binding01_sub05 Update not needed
Run: 008 ----------------
Mon Apr 17 15:07:38 EDT 2017
170412_xu_binding01_sub05 008 Update not needed
Run: 010 ----------------
Mon Apr 17 15:07:38 EDT 2017
170412_xu_binding01_sub05 010 Update not needed
Run: 012 ----------------
Mon Apr 17 15:07:38 EDT 2017
170412_xu_binding01_sub05 012 Update not needed
Run: 020 ----------------
Mon Apr 17 15:07:38 EDT 2017
170412_xu_binding01_sub05 020 Update not needed
Run: 022 ----------------
Mon Apr 17 15:07:38 EDT 2017
170412_xu_binding01_sub05 022 Update not needed
Run: 024 ----------------
Mon Apr 17 15:07:38 EDT 2017
170412_xu_binding01_sub05 024 Update not needed
Run: 034 ----------------
Mon Apr 17 15:07:38 EDT 2017
170412_xu_binding01_sub05 034 Update not needed
Run: 036 ----------------
Mon Apr 17 15:07:39 EDT 2017
170412_xu_binding01_sub05 036 Update not needed
Run: 038 ----------------
Mon Apr 17 15:07:39 EDT 2017
170412_xu_binding01_sub05 038 Update not needed
Run: 046 ----------------
Mon Apr 17 15:07:39 EDT 2017
170412_xu_binding01_sub05 046 Update not needed
Run: 048 ----------------
Mon Apr 17 15:07:39 EDT 2017
170412_xu_binding01_sub05 048 Update not needed
Run: 050 ----------------
Mon Apr 17 15:07:39 EDT 2017
170412_xu_binding01_sub05 050 Update not needed
Mon Apr 17 15:07:39 EDT 2017
mktemplate-sess completed
170412_xu_binding01_sub05 Mask ------------------------
mkbrainmask-sess -maskstem brain -fsd bold -s 170412_xu_binding01_sub05 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -rlf runlist_double.txt -nolog -update
------------------------------------------------
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170412_xu_binding01_sub05
Mon Apr 17 15:07:39 EDT 2017
170412_xu_binding01_sub05 Update not needed for session-level mask
170412_xu_binding01_sub05 Update not needed for run 008 mask
170412_xu_binding01_sub05 Update not needed for run 008 meanval
170412_xu_binding01_sub05 Update not needed for run 010 mask
170412_xu_binding01_sub05 Update not needed for run 010 meanval
170412_xu_binding01_sub05 Update not needed for run 012 mask
170412_xu_binding01_sub05 Update not needed for run 012 meanval
170412_xu_binding01_sub05 Update not needed for run 020 mask
170412_xu_binding01_sub05 Update not needed for run 020 meanval
170412_xu_binding01_sub05 Update not needed for run 022 mask
170412_xu_binding01_sub05 Update not needed for run 022 meanval
170412_xu_binding01_sub05 Update not needed for run 024 mask
170412_xu_binding01_sub05 Update not needed for run 024 meanval
170412_xu_binding01_sub05 Update not needed for run 034 mask
170412_xu_binding01_sub05 Update not needed for run 034 meanval
170412_xu_binding01_sub05 Update not needed for run 036 mask
170412_xu_binding01_sub05 Update not needed for run 036 meanval
170412_xu_binding01_sub05 Update not needed for run 038 mask
170412_xu_binding01_sub05 Update not needed for run 038 meanval
170412_xu_binding01_sub05 Update not needed for run 046 mask
170412_xu_binding01_sub05 Update not needed for run 046 meanval
170412_xu_binding01_sub05 Update not needed for run 048 mask
170412_xu_binding01_sub05 Update not needed for run 048 meanval
170412_xu_binding01_sub05 Update not needed for run 050 mask
170412_xu_binding01_sub05 Update not needed for run 050 meanval
Mon Apr 17 15:07:41 EDT 2017
mkbrainmask-sess done
170412_xu_binding01_sub05 Registration -----------------------------
register-sess -s 170412_xu_binding01_sub05 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
--------------------------------------------------------------
register-sess logfile is /dev/null
--------------------------------------------------------------
Mon Apr 17 15:07:41 EDT 2017
setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
cd /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
/ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/register-sess -s 170412_xu_binding01_sub05 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170412_xu_binding01_sub05 ----------------
Mon Apr 17 15:07:41 EDT 2017
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170412_xu_binding01_sub05
Mon Apr 17 15:07:42 EDT 2017
register-sess completed
170412_xu_binding01_sub05 MC -----------------------------
mc-sess -fstem f -fmcstem fmc -s 170412_xu_binding01_sub05 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -per-session -nolog -update
Logfile is /dev/null
-------------------------------------------
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170412_xu_binding01_sub05
RunList: 008 010 012 020 022 024 034 036 038 046 048 050
170412_xu_binding01_sub05 008 Update not needed
170412_xu_binding01_sub05 010 Update not needed
170412_xu_binding01_sub05 012 Update not needed
170412_xu_binding01_sub05 020 Update not needed
170412_xu_binding01_sub05 022 Update not needed
170412_xu_binding01_sub05 024 Update not needed
170412_xu_binding01_sub05 034 Update not needed
170412_xu_binding01_sub05 036 Update not needed
170412_xu_binding01_sub05 038 Update not needed
170412_xu_binding01_sub05 046 Update not needed
170412_xu_binding01_sub05 048 Update not needed
170412_xu_binding01_sub05 050 Update not needed
Mon Apr 17 15:07:42 EDT 2017
mc-sess completed SUCCESSFULLY
----------------------------------------
Started at Mon Apr 17 15:07:38 EDT 2017
Ended at Mon Apr 17 15:07:42 EDT 2017
preproc-sess done
preproc-sess -s 170416_xu_binding01_sub06 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog
--------------------------------------------------------------
preproc-sess logfile is /dev/null
--------------------------------------------------------------
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
jtaylor
setenv FREESURFER_HOME /ncf/nrg/sw/apps/freesurfer/5.3.0
setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
/ncf/vcn/jtaylor/programs/batch_edits/preproc-sess
-s 170416_xu_binding01_sub06 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog
Mon Apr 17 15:07:43 EDT 2017
instem f
mc 1 f fmc
stc 0 fmc
sm 0 fmc
mask 1 brain
170416_xu_binding01_sub06 Template -----------------------------
mktemplate-sess -s 170416_xu_binding01_sub06 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -nolog -update
Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170416_xu_binding01_sub06 ----------------
Mon Apr 17 15:07:43 EDT 2017
Detected input format at nii.gz
170416_xu_binding01_sub06 Update not needed
Run: 014 ----------------
Mon Apr 17 15:07:43 EDT 2017
170416_xu_binding01_sub06 014 Update not needed
Run: 016 ----------------
Mon Apr 17 15:07:43 EDT 2017
170416_xu_binding01_sub06 016 Update not needed
Run: 018 ----------------
Mon Apr 17 15:07:43 EDT 2017
170416_xu_binding01_sub06 018 Update not needed
Run: 026 ----------------
Mon Apr 17 15:07:43 EDT 2017
170416_xu_binding01_sub06 026 Update not needed
Run: 028 ----------------
Mon Apr 17 15:07:43 EDT 2017
170416_xu_binding01_sub06 028 Update not needed
Run: 030 ----------------
Mon Apr 17 15:07:43 EDT 2017
170416_xu_binding01_sub06 030 Update not needed
Run: 040 ----------------
Mon Apr 17 15:07:44 EDT 2017
170416_xu_binding01_sub06 040 Update not needed
Run: 042 ----------------
Mon Apr 17 15:07:44 EDT 2017
170416_xu_binding01_sub06 042 Update not needed
Run: 044 ----------------
Mon Apr 17 15:07:44 EDT 2017
170416_xu_binding01_sub06 044 Update not needed
Run: 052 ----------------
Mon Apr 17 15:07:44 EDT 2017
170416_xu_binding01_sub06 052 Update not needed
Run: 054 ----------------
Mon Apr 17 15:07:44 EDT 2017
170416_xu_binding01_sub06 054 Update not needed
Run: 056 ----------------
Mon Apr 17 15:07:44 EDT 2017
170416_xu_binding01_sub06 056 Update not needed
Mon Apr 17 15:07:44 EDT 2017
mktemplate-sess completed
170416_xu_binding01_sub06 Mask ------------------------
mkbrainmask-sess -maskstem brain -fsd bold -s 170416_xu_binding01_sub06 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -rlf runlist_double.txt -nolog -update
------------------------------------------------
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170416_xu_binding01_sub06
Mon Apr 17 15:07:44 EDT 2017
170416_xu_binding01_sub06 Update not needed for session-level mask
170416_xu_binding01_sub06 Update not needed for run 014 mask
170416_xu_binding01_sub06 Update not needed for run 014 meanval
170416_xu_binding01_sub06 Update not needed for run 016 mask
170416_xu_binding01_sub06 Update not needed for run 016 meanval
170416_xu_binding01_sub06 Update not needed for run 018 mask
170416_xu_binding01_sub06 Update not needed for run 018 meanval
170416_xu_binding01_sub06 Update not needed for run 026 mask
170416_xu_binding01_sub06 Update not needed for run 026 meanval
170416_xu_binding01_sub06 Update not needed for run 028 mask
170416_xu_binding01_sub06 Update not needed for run 028 meanval
170416_xu_binding01_sub06 Update not needed for run 030 mask
170416_xu_binding01_sub06 Update not needed for run 030 meanval
170416_xu_binding01_sub06 Update not needed for run 040 mask
170416_xu_binding01_sub06 Update not needed for run 040 meanval
170416_xu_binding01_sub06 Update not needed for run 042 mask
170416_xu_binding01_sub06 Update not needed for run 042 meanval
170416_xu_binding01_sub06 Update not needed for run 044 mask
170416_xu_binding01_sub06 Update not needed for run 044 meanval
170416_xu_binding01_sub06 Update not needed for run 052 mask
170416_xu_binding01_sub06 Update not needed for run 052 meanval
170416_xu_binding01_sub06 Update not needed for run 054 mask
170416_xu_binding01_sub06 Update not needed for run 054 meanval
170416_xu_binding01_sub06 Update not needed for run 056 mask
170416_xu_binding01_sub06 Update not needed for run 056 meanval
Mon Apr 17 15:07:47 EDT 2017
mkbrainmask-sess done
170416_xu_binding01_sub06 Registration -----------------------------
register-sess -s 170416_xu_binding01_sub06 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
--------------------------------------------------------------
register-sess logfile is /dev/null
--------------------------------------------------------------
Mon Apr 17 15:07:47 EDT 2017
setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
cd /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
/ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/register-sess -s 170416_xu_binding01_sub06 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170416_xu_binding01_sub06 ----------------
Mon Apr 17 15:07:47 EDT 2017
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170416_xu_binding01_sub06
Mon Apr 17 15:07:47 EDT 2017
register-sess completed
170416_xu_binding01_sub06 MC -----------------------------
mc-sess -fstem f -fmcstem fmc -s 170416_xu_binding01_sub06 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -per-session -nolog -update
Logfile is /dev/null
-------------------------------------------
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170416_xu_binding01_sub06
RunList: 014 016 018 026 028 030 040 042 044 052 054 056
170416_xu_binding01_sub06 014 Update not needed
170416_xu_binding01_sub06 016 Update not needed
170416_xu_binding01_sub06 018 Update not needed
170416_xu_binding01_sub06 026 Update not needed
170416_xu_binding01_sub06 028 Update not needed
170416_xu_binding01_sub06 030 Update not needed
170416_xu_binding01_sub06 040 Update not needed
170416_xu_binding01_sub06 042 Update not needed
170416_xu_binding01_sub06 044 Update not needed
170416_xu_binding01_sub06 052 Update not needed
170416_xu_binding01_sub06 054 Update not needed
170416_xu_binding01_sub06 056 Update not needed
Mon Apr 17 15:07:47 EDT 2017
mc-sess completed SUCCESSFULLY
----------------------------------------
Started at Mon Apr 17 15:07:43 EDT 2017
Ended at Mon Apr 17 15:07:47 EDT 2017
preproc-sess done
-------------------------------------------
/net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01
Mon Apr 17 15:07:48 EDT 2017
anadir = /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01/bold/glm_double_all_ps_0
ERROR: cannot find /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01/bold/008/fmc.sm0
On Fri, Apr 7, 2017 at 12:00 PM, <freesurfer-request@nmr.mgh.harvard.edu > wrote:
Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at
freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. postdoctoral Research Fellow position at Mayo Clinic
(Senjem, Matthew L., M.S.)
2. First-level GLM on externally-preprocessed functionals
(Christopher Markiewicz)
3. Re: Custom color maps (Senften, Peter)
4. Re: MRIread (load_nifti)- Out of memory (Bruce Fischl)
5. Re: long mri_ca_register error (Bruce Fischl)
6. Re: help (Bruce Fischl)
7. Re: MRIread (load_nifti)- Out of memory (Ilaria Sani)
8. Re: MRIread (load_nifti)- Out of memory (Douglas N Greve)
9. Re: QDEC-volume, thickness and area (Douglas N Greve)
10. Re: Help on "mris_anatomical_stats" (Douglas N Greve)
11. Re: First-level GLM on externally-preprocessed functionals
(Douglas N Greve)
12. Re: Custom color maps (Douglas N Greve)
13. Re: Custom registration template (Douglas N Greve)
14. Re: Selxavg3-sess Looking for (and can't find) "fmc.sm0"
(Douglas N Greve)
15. Re: Ventricle-to-Brain Ratio (Douglas N Greve)
16. Re: ROI seed size (Douglas N Greve)
17. Re: correlation coefficient R (Douglas N Greve)
18. Re: Custom color maps (Senften, Peter)
19. Re: General QDEC clarification queastions (Douglas N Greve)
20. QDEC and ROI drawing (Arnaud Bor?)
21. Re: QDEC and ROI drawing (Douglas N Greve)
22. Re: QDEC-volume, thickness and area (Lim, Lena)
23. Re: QDEC-volume, thickness and area (Douglas N Greve)
24. R: Re: R: R: Re: R: Re: Whole preprocessing with FAST without
to perform a seed based analysis (stdp82@virgilio.it)
25. Re: R: Re: R: R: Re: R: Re: Whole preprocessing with FAST
without to perform a seed based analysis (Douglas N Greve)
26. QDEC-Cortical Thickness (Limachia, Gaurang (NIH/NINDS) [F])
27. Re: Custom registration template (Linda Zhang)
28. Re: Ventricle-to-Brain Ratio (Gullickson, James)
29. Re: MRIread (load_nifti)- Out of memory (Ilaria Sani)
30. Re: long mri_ca_register error (Chris Adamson)
31. Re: help (Dilip Puri)
32. How to segment subnuclei of thalamus? (Shane S)
33. withdrawing from the mailing list. (kjunji@med.kanazawa-u.ac.jp)
34. Re: QA Tools v1.2 and future release (Yong Li)
35. Hippocampal subfield segmentation, file content (Nina Jacobsen)
36. Re: Multiple Comparisons Correction thresh error (teodora petrova)
37. Longitudinal Pipeline (Arman Eshaghi)
38. Re: Hippocampal subfield segmentation, file content
(Iglesias Gonzalez, Eugenio)
39. Re: How to segment subnuclei of thalamus? (Bruce Fischl)
40. Analyzing xhemi results (Marissa Pifer)
41. Re: QDEC and ROI drawing (Arnaud Bor?)
------------------------------------------------------------ ----------
Message: 1
Date: Thu, 06 Apr 2017 16:17:30 +0000
From: "Senjem, Matthew L., M.S." <Senjem.Matthew1@mayo.edu>
Subject: [Freesurfer] postdoctoral Research Fellow position at Mayo
Clinic
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID: <47cabe$66564f@ironport10.mayo.edu >
Content-Type: text/plain; charset="windows-1252"
The Mayo Clinic Departments of Neurology and Diagnostic Radiology in Rochester, Minnesota are seeking applications for a fully-funded, two-year postdoctoral Research Fellow position to begin in July of 2017. The Research Fellow position will primarily work on developing advanced multi-modal molecular and high-field (3T and 7T) neuroimaging to study connectomics in pre-clinical and clinical Alzheimer?s disease. The resulting data will be acquired and analyzed as part of a unique collaboration between investigators at Mayo Clinic Alzheimer?s Disease Research Center and the Center for Magnetic Resonance Research at the University of Minnesota. Basic programing skills and familiarity with widely used neuroimaging software platforms are required for successful applicants. Familiarity with the Human Connectome Project imaging and analyses protocols is preferred but not required. No clinical or Alzheimer?s specific background is required. Salary will be commensurate with postdoctoral experience. The position will remain open until filled by a successful candidate.
Please send CV, three letters of recommendation, and any inquiries to:
David T. Jones, M.D.
Mayo Clinic
Department of Neurology
Email: Jones.David@mayo.edu<mailto:Jones.David@mayo.edu >
A Research Fellow at Mayo Clinic is a temporary position intended to provide training and education in research. Individuals will train in the research program of a Mayo Clinic principal investigator. Qualified individuals will demonstrate the potential for research as evidenced by their training and peer-reviewed publications and should become competitive for national research grants. Proof of English proficiency is required for J-1 Short-Term Scholars, Research Scholars, Professors, Specialists, and Student Interns sponsored by Mayo Clinic.
Why Mayo Clinic? Learn and grow among the best in your field at the nation?s top hospital (U.S. News & World Report, 2016-2017), ranked No. 1 in more specialties than any other care provider. Mayo Clinic is committed to sustaining and growing research, believes in research-driven care and establishes a well-defined integration between the clinical practice and research. At Mayo Clinic, you?ll use the power of collaboration to achieve the highest standards for medical care and health improvement, working in the largest integrated, not-for-profit medical group practice in the world with over 60,000 employees. You?re invited to contribute to a unique environment that brings together the best in patient care, groundbreaking research and innovative medical education. We offer exceptional benefits, and have been recognized by FORTUNE magazine as one of the top 100 ?Best Companies to Work For?.
Mayo Clinic is an equal opportunity educator and employer (including veterans and persons with disabilities).
------------------------------------------------------------ ------------------------------ ------------------------------ ------------------------------ -------------------
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------------------------------
Message: 2
Date: Thu, 6 Apr 2017 12:35:05 -0400
From: Christopher Markiewicz <effigies@bu.edu>
Subject: [Freesurfer] First-level GLM on externally-preprocessed
functionals
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<CAHE-diMQn+WO5VdzmFYhoBm2C7kRCdU=4kOHrAL9hdFqhO1Wcw@mail. gmail.com >
Content-Type: text/plain; charset="utf-8"
Hi list,
We're working on making a preprocessing stream that will be generally
accessible to different analysis streams, including FreeSurfer. One
component of this is sampling functional volumes to FreeSurfer meshes, and
I want to test this component by running a simple first-level GLM in
FreeSurfer.
I've always done this through the FSFAST pipeline, but that may be a bit
much, given that I'm starting from surface time series (the equivalent of
`$FUNCTIONALS_DIR/$SESS_ID/bold/$RUN/fmcpr.sm0.fsaverage.lh. nii.gz`, but as
a GIFTI file).
Supposing I have a paradigm file and the files described above, what's the
best way to do a basic GLM? Would it be to `mri_surf2surf` our GIFTI
surfaces into `fmcpr.sm0.fsaverage.lh.nii.gz` files in a FSFAST directory
structure, and pick up at `mkanalysis-sess`? Or is there a more
straightforward way to just get a simple set of contrasts to compare with a
volumetric analysis?
Thanks in advance,
Chris Markiewicz
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------------------------------
Message: 3
Date: Thu, 6 Apr 2017 17:00:18 +0000
From: "Senften, Peter" <peter.senften@ubc.ca>
Subject: Re: [Freesurfer] Custom color maps
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<B6AC19D7BE198443A028636599CB88771E558248@exch-mbx08p.ead.ub >c.ca
Content-Type: text/plain; charset="us-ascii"
hi,
I've read through the list, and searched over the last few days, and can't quite seem to find what I'm looking for. My first message wasn't clear at all either (my apologies), it was one of those days where your brain ends up in a bit of a fog.
I am trying to get a heat map style visual output based on the destrieux 72 region map using cortical thickness as our measure. I'm using FS 6.0 and the edits and outputs have all gone great. We are doing the analysis of the cortical thickness outside of FS and would like to create a heat-map style visual output of the areas that show a large effect size. My original idea was to create a custom color map and somehow load that in place of the default destrieux color map but I couldn't get that to work. Tried replacing the FS LUT table as well and when loaded the colors remained the same as well.
Hope that clarifies what I'm trying to do.
Thanks,
Peter
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu ] on behalf of dg wakeman [dgwakeman@gmail.com]
Sent: Tuesday, April 04, 2017 12:11 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Custom color maps
Hi Peter,
We will need a lot more details to help. I suggest you look through
the e-mail list a bit. I spent a lot of time helping a user or two
with a similar issue. The key details are what are you trying to show
(an annotation, a single label, or values)?
hth
d
On Wed, Mar 29, 2017 at 11:15 AM, Senften, Peter <peter.senften@ubc.ca> wrote:
> Hello,
>
> I am wondering if it is possible to create a custom color map that will be
> visible in freeview using the 3D viewer - not the coronal, axial, or sagital
> views. I created a copy of the LUT file and then replaced the RGB values the
> ones I wanted but haven't been able to get it to load at all.
>
> In the end I am trying to make pretty 3D pictures to see our regions of
> interest better for our data. I am open to other ways of doing this.
>
> Thanks,
>
> Peter
>
> _______________________________________________
> 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
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 4
Date: Thu, 6 Apr 2017 13:35:31 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<alpine.LRH.2.20.1704061335010.29155@gate.nmr.mgh.harvard. >edu
Content-Type: text/plain; charset="iso-8859-7"
Hi Ilaria
do you have any reason to believe that it isn't just out of memory? If so,
there's not much to do other than get more RAM or use a different machine
cheers
Bruce
On Thu,
6 Apr 2017, Ilaria Sani wrote:
>
> Dear All,
>
> ?
>
> I?m trying to load a pretty big diffusion MRI dataset (320x320x260x122).
>
> I?m running matlab 2015a 64bit on a linux machine.
>
> ?
>
> I?m using MRIread, which in turn calls load_nifti.
>
> I?m getting the following error:
>
> ?
>
> Error using? +
>
> Out of memory. Type HELP MEMORY for your options.
>
> ?
>
> Error in load_nifti (line 158)
>
> ? hdr.vol = hdr.vol * hdr.scl_slope? + hdr.scl_inter;
>
> ?
>
> Error in MRIread (line 158)
>
> hdr = load_nifti(fspec,headeronly);
>
> ?
>
> When I load half dataset (320x320x260x61) it works ok.
>
> I tried to increase the Maximum array size in Matalb (default 1,000 - now 10,000), but I?m still getting the error.
>
> I tried to change machine (which runs matlab 2013a on linux) and it worked fine.
>
> ?
>
> I think this is due to some matlab settings.
>
> Can anyone help?
>
> ?
>
> Thanks a lot,
>
> Ilaria
>
> ?
>
> ?
>
> -------------------------------------------
> Ilaria Sani, PhD
> Postdoctoral Fellow, Freiwald Lab
> The Rockefeller University
> 1230 York Ave., New York, NY 10065.
> Phone: (212) 327?7699
> Fax: ??? (212) 327 7698
> Email:?isani01@rockefeller.edu
>
> ?
>
>
>
------------------------------
Message: 5
Date: Thu, 6 Apr 2017 13:37:14 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] long mri_ca_register error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<alpine.LRH.2.20.1704061336540.29155@gate.nmr.mgh.harvard. >edu
Content-Type: text/plain; charset="iso-8859-7"
Hi Chris
it's possible we never looked at -bigventricle in the long stage. What
was your recon-all command line?
cheers
Bruce
On Thu, 6 Apr 2017, Chris Adamson wrote:
>
> It happens when I use -bigventricles.
>
> ?
>
> From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu ] On Behalf Of Chris Adamson
> Sent: Thursday, 6 April 2017 12:27 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] long mri_ca_register error
>
> ?
>
> Freesurfer devs,
>
> ?
>
> In freesurfer 6 stable I?m having a problem at the careg stage of the long. The relevant recon-all log is pasted below. Could you point me to where to debug this
> problem?
>
> ?
>
> Cheers,
>
> ?
>
> Chris.
>
> ?
>
> mri_ca_register -rusage 136_S_0426_20070604.long.136_S_0426/touch/rusage.mri_ca_regi ster.dat -bigventricles -smoothness 0.5 -levels 2 -A 1 -l
> *base*/transforms/talairach.m3z identity.nofile -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer-6.0.0/av erage/RB_all_2016-05-10.vc700. gca
> transforms/talairach.m3z
>
> ?
>
> handling expanded ventricles...
>
> l_smoothness = 0.50
>
> levels = 2
>
> smoothing gradient with 1 averages...
>
> reading previously computed atlas xform /isilon/data/addo/ADNI3T/freesurfer6/136_S_0426/mri/transfor ms/talairach.m3z and applying inverse registration identity.nofile
>
> renormalizing sequences with structure alignment, equivalent to:
>
> ??? -renormalize
>
> ??? -regularize_mean 0.500
>
> ??? -regularize 0.500
>
> using MR volume brainmask.mgz to mask input volume...
>
> ?
>
> == Number of threads available to mri_ca_register for OpenMP = 2 ==
>
> reading 1 input volumes...
>
> logging results to talairach.log
>
> reading input volume 'norm.mgz'...
>
> reading GCA '/usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700 .gca'...
>
> label assignment complete, 0 changed (0.00%)
>
> TransformSample: gcam has not been inverted!
>
> freeing gibbs priors...done.
>
> average std[0] = 5.0
>
> setting orig areas to linear transform determinant scaled 8.40
>
> writing talairach.invalid.mgz
>
> writing talairach.status.mgz
>
> registering ventricular system...
>
> using threshold 45.0 from atlas ventricle (20.1 +- 5.0) and caudate (70.0 +- 5.0) distributions for initial ventricular estimate
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> ?
>
> Dr Chris Adamson
>
> Senior Research Officer
>
> Developmental Imaging, Clinical Sciences
>
> ?
>
> Murdoch Childrens Research Institute
>
> The Royal Children?s Hospital
>
> Flemington Road, Parkville, VIC 3052 Australia
>
> E?chris.adamson@mcri.edu.au?
>
> www.mcri.edu.au
>
> ?
>
> ?
>
> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the
> intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail,
> and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated
> to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the
> integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.
>
> ?
>
> P?Please consider the environment before?printing this email
>
> ?
>
>
> ____________________________________________________________ __________
> This email has been scanned by the Symantec Email Security.cloud service.
> For more information please visit http://www.symanteccloud.com
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------------------------------
Message: 6
Date: Thu, 6 Apr 2017 13:38:20 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] help
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<alpine.LRH.2.20.1704061338010.29155@gate.nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi Dilip
yes, freesurfer will do this for you, although the labels will be 17 for
left hippocampus and 53 for right.
cheers
Bruce
On Thu, 6 Apr 2017, Dilip Puri wrote:
> Hi everyone,
>
> I am working on Hippocampus segmentation using Neural Networks for that I need labeled images of Hippocampus corresponding to original images.
>
> I am using OASIS Dataset for this. I want to generate labeled images using FREESURFER. Is there any way to label each 3D co-ordinate
> HippoCampus -1
> Otherwise - 0
>
> Here are sample files link
>
> Kindly help me!
>
>
> Dilip Puri
> IIIT Vadodara
>
>
------------------------------
Message: 7
Date: Thu, 6 Apr 2017 18:53:34 +0000
From: Ilaria Sani <isani01@mail.rockefeller.edu>
Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID: <83430b6af8e142319c5cdbf9cb130b2a@RUMBX12.rockefeller.edu >
Content-Type: text/plain; charset="iso-8859-7"
Hi Bruce,
Not sure this answer your question...
In matlab workspace, I am able to load data in two halves:
H1=MRIread(half1)
H2=MRIread(half2)
And then concatenate the volumes
concatenate them var=cat(4,H1,H2).
So, somehow matlab can handle...
However, when those operations are embedded inside a function (like in the case of load_nifti and MRIread) I get the error.
Thanks,
Ilaria
-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu ] On Behalf Of Bruce Fischl
Sent: Thursday, April 6, 2017 1:36 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
Hi Ilaria
do you have any reason to believe that it isn't just out of memory? If so, there's not much to do other than get more RAM or use a different machine
cheers
Bruce
On Thu,
6 Apr 2017, Ilaria Sani wrote:
>
> Dear All,
>
> ?
>
> I?m trying to load a pretty big diffusion MRI dataset (320x320x260x122).
>
> I?m running matlab 2015a 64bit on a linux machine.
>
> ?
>
> I?m using MRIread, which in turn calls load_nifti.
>
> I?m getting the following error:
>
> ?
>
> Error using? +
>
> Out of memory. Type HELP MEMORY for your options.
>
> ?
>
> Error in load_nifti (line 158)
>
> ? hdr.vol = hdr.vol * hdr.scl_slope? + hdr.scl_inter;
>
> ?
>
> Error in MRIread (line 158)
>
> hdr = load_nifti(fspec,headeronly);
>
> ?
>
> When I load half dataset (320x320x260x61) it works ok.
>
> I tried to increase the Maximum array size in Matalb (default 1,000 - now 10,000), but I?m still getting the error.
>
> I tried to change machine (which runs matlab 2013a on linux) and it worked fine.
>
> ?
>
> I think this is due to some matlab settings.
>
> Can anyone help?
>
> ?
>
> Thanks a lot,
>
> Ilaria
>
> ?
>
> ?
>
> -------------------------------------------
> Ilaria Sani, PhD
> Postdoctoral Fellow, Freiwald Lab
> The Rockefeller University
> 1230 York Ave., New York, NY 10065.
> Phone: (212) 327?7699
> Fax: ??? (212) 327 7698
> Email:?isani01@rockefeller.edu
>
> ?
>
>
>
------------------------------
Message: 8
Date: Thu, 6 Apr 2017 15:42:31 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <9df0ba99-7c57-7370-e278-6f0a8ff9b0f8@nmr.mgh.harvard.edu >
Content-Type: text/plain; charset=iso-8859-7; format=flowed
is it a compressed nifti (nii.gz)? If so, try uncompressing it first
On 04/06/2017 02:53 PM, Ilaria Sani wrote:
> Hi Bruce,
>
> Not sure this answer your question...
>
> In matlab workspace, I am able to load data in two halves:
>
> H1=MRIread(half1)
> H2=MRIread(half2)
>
> And then concatenate the volumes
> concatenate them var=cat(4,H1,H2).
>
> So, somehow matlab can handle...
>
> However, when those operations are embedded inside a function (like in the case of load_nifti and MRIread) I get the error.
>
>
> Thanks,
> Ilaria
>
>
> -----Original Message-----
> From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu ] On Behalf Of Bruce Fischl
> Sent: Thursday, April 6, 2017 1:36 PM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
> Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
>
> Hi Ilaria
>
> do you have any reason to believe that it isn't just out of memory? If so, there's not much to do other than get more RAM or use a different machine
>
> cheers
> Bruce
>
>
> On Thu,
> 6 Apr 2017, Ilaria Sani wrote:
>
>> Dear All,
>>
>>
>>
>> I?m trying to load a pretty big diffusion MRI dataset (320x320x260x122).
>>
>> I?m running matlab 2015a 64bit on a linux machine.
>>
>>
>>
>> I?m using MRIread, which in turn calls load_nifti.
>>
>> I?m getting the following error:
>>
>>
>>
>> Error using +
>>
>> Out of memory. Type HELP MEMORY for your options.
>>
>>
>>
>> Error in load_nifti (line 158)
>>
>> hdr.vol = hdr.vol * hdr.scl_slope + hdr.scl_inter;
>>
>>
>>
>> Error in MRIread (line 158)
>>
>> hdr = load_nifti(fspec,headeronly);
>>
>>
>>
>> When I load half dataset (320x320x260x61) it works ok.
>>
>> I tried to increase the Maximum array size in Matalb (default 1,000 - now 10,000), but I?m still getting the error.
>>
>> I tried to change machine (which runs matlab 2013a on linux) and it worked fine.
>>
>>
>>
>> I think this is due to some matlab settings.
>>
>> Can anyone help?
>>
>>
>>
>> Thanks a lot,
>>
>> Ilaria
>>
>>
>>
>>
>>
>> -------------------------------------------
>> Ilaria Sani, PhD
>> Postdoctoral Fellow, Freiwald Lab
>> The Rockefeller University
>> 1230 York Ave., New York, NY 10065.
>> Phone: (212) 327 7699
>> Fax: (212) 327 7698
>> Email: isani01@rockefeller.edu
>>
>>
>>
>>
>>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
------------------------------
Message: 9
Date: Thu, 6 Apr 2017 15:45:11 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] QDEC-volume, thickness and area
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <d88bff3e-9ece-5b51-3e12-2ed44ebbc5c9@nmr.mgh.harvard.edu >
Content-Type: text/plain; charset=windows-1252; format=flowed
what do you mean they do not differ in gender ratio? Just that the
relative number of M/F is the same in each group? If there is not a
significant interaction between gender and group, then you can usually
merge the genders.
On 04/05/2017 05:13 PM, Lim, Lena wrote:
>
> Dear Freesurfer Experts,
>
> 1) I have 2 groups (A & B), which do not differ in terms of gender
> ratio. If there were no significant regions for Group-Gender
> interaction in mean cortical thickness in the QDEC analysis, can I
> conclude that gender does not influence the effect of group on
> thickness? The differences between A and B on mean thickness is not
> affected by Gender? Is this valid or do I need to add Gender as a
> covariate even though the group do not differ on gender ratio?
>
> 2) A reviewer pointed that it is not right to test for group
> differences in volume once I have tested for thickness and area,
> especially when there is a cluster where A and B do not differ
> significantly in thickness and area but they differ significantly in
> volume?Is this right?
>
> Please kindly advise.
>
> Many thanks,
>
> Lena
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
------------------------------
Message: 10
Date: Thu, 6 Apr 2017 15:55:39 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Help on "mris_anatomical_stats"
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <f99aa257-7ad7-61e8-dd0f-7d63615b3aaa@nmr.mgh.harvard.edu >
Content-Type: text/plain; charset=windows-1252; format=flowed
I can't replicate. Try loading the white and pial surfaces into
freeview. If that works, please upload your subject so I can try to
replicate the error
On 12/08/2015 11:22 AM, Lim, Lena wrote:
>
> Dear Experts,
>
> I ran a group analysis in Qdec for the left volume and found a region
> of significant group difference. I wanted to extract this ROI. I
> defined this label and used the ?map label to subjects? option in Qdec
> and ran the following but encountered the following error. Please
> kindly help?
>
> [spjwker@nanlnx2 FSL]1% mris_anatomical_stats ?l lh.HCA_vol.label \-b
> -f PAC07/stats/lh.HCA_vol.stats PAC07 lh
>
> limiting computations to label lh.HCA_vol.label.
>
> reading volume /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/mri/wm.mgz...
>
> reading input surface
> /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.white...
>
> reading input pial surface
> /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.pial...
>
> reading input white surface
> /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.white...
>
> Segmentation fault
>
> Many thanks,
>
> Lena
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
------------------------------
Message: 11
Date: Thu, 6 Apr 2017 15:58:47 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] First-level GLM on externally-preprocessed
functionals
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <08302d8d-6dd8-9896-7072-4651d953a497@nmr.mgh.harvard.edu >
Content-Type: text/plain; charset=windows-1252; format=flowed
You should be able to do it that way. When you run mkanalysis, specify
-funcstem fmcpr.sm0.fsaverage.lh.nii.gz, and then selxavg3-sess will
then use that file as input. If you want to smooth, then do that
explicitly and pass the smoothed file to mkanalysis
On 04/06/2017 12:35 PM, Christopher Markiewicz wrote:
> Hi list,
>
> We're working on making a preprocessing stream that will be generally
> accessible to different analysis streams, including FreeSurfer. One
> component of this is sampling functional volumes to FreeSurfer meshes,
> and I want to test this component by running a simple first-level GLM
> in FreeSurfer.
>
> I've always done this through the FSFAST pipeline, but that may be a
> bit much, given that I'm starting from surface time series (the
> equivalent of
> `$FUNCTIONALS_DIR/$SESS_ID/bold/$RUN/fmcpr.sm0.fsaverage.lh. nii.gz`,
> but as a GIFTI file).
>
> Supposing I have a paradigm file and the files described above, what's
> the best way to do a basic GLM? Would it be to `mri_surf2surf` our
> GIFTI surfaces into `fmcpr.sm0.fsaverage.lh.nii.gz` files in a FSFAST
> directory structure, and pick up at `mkanalysis-sess`? Or is there a
> more straightforward way to just get a simple set of contrasts to
> compare with a volumetric analysis?
>
> Thanks in advance,
> Chris Markiewicz
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
------------------------------
Message: 12
Date: Thu, 6 Apr 2017 16:00:08 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Custom color maps
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <fa3b5c5d-ed71-9b8a-7b13-5d101908bc91@nmr.mgh.harvard.edu >
Content-Type: text/plain; charset=windows-1252; format=flowed
See if annotval2surfoverlay.m does what you want. It is in v6. If you
have v5.x, I can send you the mfile separtely
On 04/06/2017 01:00 PM, Senften, Peter wrote:
> hi,
>
> I've read through the list, and searched over the last few days, and can't quite seem to find what I'm looking for. My first message wasn't clear at all either (my apologies), it was one of those days where your brain ends up in a bit of a fog.
>
> I am trying to get a heat map style visual output based on the destrieux 72 region map using cortical thickness as our measure. I'm using FS 6.0 and the edits and outputs have all gone great. We are doing the analysis of the cortical thickness outside of FS and would like to create a heat-map style visual output of the areas that show a large effect size. My original idea was to create a custom color map and somehow load that in place of the default destrieux color map but I couldn't get that to work. Tried replacing the FS LUT table as well and when loaded the colors remained the same as well.
>
> Hope that clarifies what I'm trying to do.
>
> Thanks,
>
> Peter
> ________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu ] on behalf of dg wakeman [dgwakeman@gmail.com]
> Sent: Tuesday, April 04, 2017 12:11 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Custom color maps
>
> Hi Peter,
>
> We will need a lot more details to help. I suggest you look through
> the e-mail list a bit. I spent a lot of time helping a user or two
> with a similar issue. The key details are what are you trying to show
> (an annotation, a single label, or values)?
>
> hth
> d
>
> On Wed, Mar 29, 2017 at 11:15 AM, Senften, Peter <peter.senften@ubc.ca> wrote:
>> Hello,
>>
>> I am wondering if it is possible to create a custom color map that will be
>> visible in freeview using the 3D viewer - not the coronal, axial, or sagital
>> views. I created a copy of the LUT file and then replaced the RGB values the
>> ones I wanted but haven't been able to get it to load at all.
>>
>> In the end I am trying to make pretty 3D pictures to see our regions of
>> interest better for our data. I am open to other ways of doing this.
>>
>> Thanks,
>>
>> Peter
>>
>> _______________________________________________
>> 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
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
------------------------------
Message: 13
Date: Thu, 6 Apr 2017 16:06:51 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Custom registration template
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <3d80e2cd-55ca-10fa-a366-94079de995cf@nmr.mgh.harvard.edu >
Content-Type: text/plain; charset=windows-1252; format=flowed
1. The "..." means to include the other options needed for the command
to run. Looks like you figured it out. Using -f as you have is correct.
2. can you send the full terminal output?
On 04/06/2017 08:55 AM, Linda Zhang wrote:
> Dear all,
>
> I've been following the instructions for building a custom
> registration template as written here
> (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTempl ) andates
> here
> (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011 ).-May/018345.html
>
>
> I'm now at the mris_preproc stage and according to the instructions,
> the command should be:
>
> # Get thickness values in the newtemplate space for GLM analysis
> mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s
> subj3 ...
>
> I put my subject list into a text file and replaced --s with --f
> [subjlist] but kept everything else the same. I got two errors for no
> source hemi specified and no output specified, so I added --hemi lh
> and --out lh.surfreg.newtemplate.thick --meas thickness. Am I
> supposed to do this, and will the output file be used for anything
> else down the line, i.e., should it be named something more specific?
> I see that the next step is to rerun the make_average_subject, but I
> don't see where the output from the mris_preproc step would figure in.
>
> On a (maybe) separate issue, when I finally ran my command line:
>
> mris_preproc --surfreg sphere.reg.newtemplate --f subjlist --hemi lh
> --out lh.surfreg.newtemplate.thick --meas thickness
>
> I got the following error:
>
> nsubjects=100
> tmpdir is ./tmp.mris_preproc.25619
> /home/fsuser/data
> set: Variable name must contain alphanumeric characters.
>
> I'm not sure where the problem might be here. I'm running FreeSurfer
> v.5.3 in Virtualbox, and I haven't had any problems while running
> recon-all on the subjects previously.
>
> Any insight would be greatly appreciated, thank you!
>
> Cheers,
> Linda
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
------------------------------
Message: 14
Date: Thu, 6 Apr 2017 16:12:31 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Selxavg3-sess Looking for (and can't find)
"fmc.sm0"
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <57429858-c90b-3267-23d5-773c1d49275d@nmr.mgh.harvard.edu >
Content-Type: text/plain; charset=windows-1252; format=flowed
can you send the full terminal output?
On 04/05/2017 04:02 PM, Taylor, Johnmark wrote:
> Hello,
>
> I am getting an odd bug on selxavg3-sess. I am getting the error message,
>
> *ERROR: cannot find [rest of file path]/fmc.sm0*
>
> I am indicating zero smoothing in mkanalysis-sess ("-fwhm 0"). I am
> confused because the output of preproc-sess for no smoothing is
> fmc.nii.gz, *NOT *fmc.sm0.nii.gz when doing analyses in native volume
> space, so I am not sure why selxavg-sess is looking for the wrong file
> path. For reference, here is my call to mkanalysis-sess:
>
> mkanalysis-sess -analysis analysis_name -fsd bold -runlistfile runlist.txt
> -native -nuisreg mcextreg 3 -fwhm 0 -event-related -nconditions 8
> -paradigm spiralpara.par -spmhrf 0 -refeventdur 12 -TR 1.5
> -polyfit 2 -nskip 8
>
> I am using Freesurfer 5.3, if that helps. The analysis works fine when
> I apply 3mm smoothing (I've done preprocessing for both the 0mm and
> 3mm options).
>
> Thank you very much, and cheers,
>
> JohnMark
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
------------------------------
Message: 15
Date: Thu, 6 Apr 2017 16:17:55 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Ventricle-to-Brain Ratio
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <b00cc093-33a4-9ae1-2e0f-637867719a68@nmr.mgh.harvard.edu >
Content-Type: text/plain; charset=windows-1252; format=flowed
that looks right. how different are the values?
On 04/05/2017 10:58 AM, Gullickson, James wrote:
> Hello all,
>
> I want to calculate a Ventricle-to-Brain ratio (VBR) as a measure of
> parenchymal atrophy using Freesurfer version 5.3.0. I have tried to go
> about this using the aseg.stats output (using asegstats2table), but am
> running into inconsistencies.
>
> The basic calculation for VBR is:
>
> (Total Ventricular Volume/Total Brain Volume) * 100
>
> i.e. Bigler, E. D. (2013). Traumatic brain injury, neuroimaging, and
> neurodegeneration. /Frontiers in human neuroscience/, /7/, 395.
>
>
> What is the best way to get Total Ventricular Volume (TVV) and Total
> Brain Volume (TBV) for this calculation? I have tried several ways,
> which lead to different values:
>
> TVV = left lateral ventricle + left inf lateral ventricle + right
> lateral ventricle + right inf lateral ventricle + 3rd ventricle + 4th
> ventricle + 5th ventricle + choroid plexus
>
> which gives me a different result than
>
> TVV = BrainSegVol - BrainSegVolNotVent
>
>
> and for TBV
>
> TBV = TotalGrayVol + CorticalWhiteMatterVol
>
> which differs from
>
> TBV = BrainSegVolNotVent
>
>
> Thank you for your help,
>
> James Gullickson
>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
------------------------------
Message: 16
Date: Thu, 6 Apr 2017 16:27:29 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] ROI seed size
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <a48d0f59-ffee-e425-f352-e382a8362116@nmr.mgh.harvard.edu >
Content-Type: text/plain; charset=utf-8; format=flowed
these are good questions without good answers. It is hard to compare
surface-based vs volume-based. The surface-based may be smaller, but it
will only include gray matter whereas a volume-based sphere will be
bigger but will include WM and CSF. If you're voxel size is small, then
3mm radius might not get more than one or two of them
On 04/03/2017 09:53 PM, ERIK JAHNER wrote:
> What is the appropriate size for a surface based seed?
>
> I am referencing a study with volumetric based seeds with spheres with a radius of 3mm (in fMRI data). I would like to do a similar study using surface based representations. In a volumetric based analysis folding may actually increase the amount of cortical surface represented in a sphere. Using a circle on the surface with a 3 mm radius therefore would not be the same. But?. is the difference so minimal and variable across the cortex that it is not worth considering especially since the seeds are derived from published work and not using a localizer?
>
> Do you know of any published guidelines on generating seed sizes in surface based models, not based on a localizer.
> Or is this the completely wrong approach? Should I be using the tal coordinates to locate which parcellation of the available atlases that the seed was located in? (for example i have a fusiform face area seed which I have set as a circle 3mm radius)
>
> many thanks for your continued help
> Erik
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
------------------------------
Message: 17
Date: Thu, 6 Apr 2017 16:31:27 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] correlation coefficient R
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <20326815-9122-4dd5-e0fa-bce6d0373e7f@nmr.mgh.harvard.edu >
Content-Type: text/plain; charset=windows-1252; format=flowed
I guess you could average it over space (eg, over a cluster). Let me
know if you want instructions. Otherwise, I'm not sure what to say.
On 04/04/2017 06:49 AM, tom parker wrote:
> Hi Doug,
> Thanks! I realize now I didn't explain myself properly.
> I need one single R value for the correlation analysis I made,
> similarly to when I correlate two variables with Pearson's R in a
> statistical package. I have a referee asking me to put it on a table
> with the freesurfer results. Is there a way to get a single average R
> value from the pcc.mgh file?
> Thank you so much!
>
> Douglas Greve
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.har >vard.edu&q=from:%22Douglas+Gre ve%22
> Mon, 03 Apr 2017 18:46:46 -0700
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.har >vard.edu&q=date:20170403
>
>
> Each vertex is a correlation value.
>
> 2017-04-04 1:09 GMT+01:00 tom parker <tomparker540@gmail.com
> <mailto:tomparker540@gmail.com>>:
>
> Thanks Doug!
>
> I have version 6 and got a pcc.mgh file.
>
> How can I get a correlation R value from this file?
>
> Thanks again
>
> Douglas N Greve
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.ha >rvard.edu&q=from:%22Douglas+N+ Greve%22
> Mon, 03 Apr 2017 09:41:41 -0700
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.ha >rvard.edu&q=date:20170403
>
>
> if you are using version 6, then it should have produced a file called
> pcc.mgh. This the partial pearson correlation coef.
>
>
>
> 2017-04-03 15:40 GMT+01:00 tom parker <tomparker540@gmail.com
> <mailto:tomparker540@gmail.com >>:
>
> Dear Freesurfers,
>
> I made some correlations between cortical thickness and age in
> qdec.
>
> Is it possible to get the correlation coefficient value of
> this analysis?
>
> I just need to put it in a table with the significant results.
>
> Thank you so much!
>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
------------------------------
Message: 18
Date: Thu, 6 Apr 2017 20:35:28 +0000
From: "Senften, Peter" <peter.senften@ubc.ca>
Subject: Re: [Freesurfer] Custom color maps
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<B6AC19D7BE198443A028636599CB88771E559AA9@exch-mbx08p.ead.ub >c.ca
Content-Type: text/plain; charset="us-ascii"
Thanks, I'll take a look at it and let you know how it goes.
Peter
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu ] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu]
Sent: Thursday, April 06, 2017 1:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Custom color maps
See if annotval2surfoverlay.m does what you want. It is in v6. If you
have v5.x, I can send you the mfile separtely
On 04/06/2017 01:00 PM, Senften, Peter wrote:
> hi,
>
> I've read through the list, and searched over the last few days, and can't quite seem to find what I'm looking for. My first message wasn't clear at all either (my apologies), it was one of those days where your brain ends up in a bit of a fog.
>
> I am trying to get a heat map style visual output based on the destrieux 72 region map using cortical thickness as our measure. I'm using FS 6.0 and the edits and outputs have all gone great. We are doing the analysis of the cortical thickness outside of FS and would like to create a heat-map style visual output of the areas that show a large effect size. My original idea was to create a custom color map and somehow load that in place of the default destrieux color map but I couldn't get that to work. Tried replacing the FS LUT table as well and when loaded the colors remained the same as well.
>
> Hope that clarifies what I'm trying to do.
>
> Thanks,
>
> Peter
> ________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu ] on behalf of dg wakeman [dgwakeman@gmail.com]
> Sent: Tuesday, April 04, 2017 12:11 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Custom color maps
>
> Hi Peter,
>
> We will need a lot more details to help. I suggest you look through
> the e-mail list a bit. I spent a lot of time helping a user or two
> with a similar issue. The key details are what are you trying to show
> (an annotation, a single label, or values)?
>
> hth
> d
>
> On Wed, Mar 29, 2017 at 11:15 AM, Senften, Peter <peter.senften@ubc.ca> wrote:
>> Hello,
>>
>> I am wondering if it is possible to create a custom color map that will be
>> visible in freeview using the 3D viewer - not the coronal, axial, or sagital
>> views. I created a copy of the LUT file and then replaced the RGB values the
>> ones I wanted but haven't been able to get it to load at all.
>>
>> In the end I am trying to make pretty 3D pictures to see our regions of
>> interest better for our data. I am open to other ways of doing this.
>>
>> Thanks,
>>
>> Peter
>>
>> _______________________________________________
>> 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
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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_______________________________________________
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 19
Date: Thu, 6 Apr 2017 16:37:11 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] General QDEC clarification queastions
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <e3752bc0-b24c-284f-a6a2-6cc5adb682b7@nmr.mgh.harvard.edu >
Content-Type: text/plain; charset=windows-1252; format=flowed
On 04/03/2017 01:45 PM, Veggeberg, Rosanna wrote:
> Hello,
> I am using QDEC to analyze cortical structural data and am looking for
> some clarification on some questions that have come up.
>
> 1. _Design tab_: In the "Measure" drop-down selection, I understand
> what we are getting when looking at thickness but the other
> measurements I am unclear on. Is there information or publications on
> the other 12 possible measures (how they are measured, what they mean,
> applications for using them). In particular, I am interested in
> learning more about area, area.pial, volume, sulc, and curv but would
> like to understand what the others mean as well to determine if they
> would be applicable to our study questions.
There is not a specific pub on this. The area is the area of a vertex
(the average of the triangles around it), same interpreation for the
volume. These are kind of like VBM analysis. area.pial is the area of
the pial surface whereas simple area is the area of the white. curv is
the curvature; sulc is the sulcal depth. These are used for registration
and generally not that interesting.
>
> 2. _Design tab_: I am a little unclear on why the model factors are
> labeled the way they are and wanted to see if I am using them correctly.
> -Discrete (Fixed Factors): this is pretty straight forward to be used
> as independent categorical variables, correct?
yes
> -Continuous (Covariate): even though it says covariate, should these
> variables just be treated as independent continuous varaibles?
correct
> -Nuisance Factors: should these just be treated as the covariates we
> wish to control for?
yes. it allows you to have more continuous variable, but you won't get
tests that include them
>
> 3. _Results_: When I am doing a group comparison (i.e. disease vs.
> control), does QDEC run the comparison based off of which order the
> labels appear in the table: disease vs. control, or does it run the
> comparison based off of which label comes first alphabetically:
> control vs. disease?
The order in your levels file
>
> 4. _Results_: When viewing the results in freeview, if I click on a
> significant cluster, in the bottom panel, does a negative value next
> to the mc-z.abs.th13.sig.cluster.mgh label indicate a decrease in
> cortical thickness (i.e. disease vs. control: negative value indicates
> control is greater than disease)?
It depends on the order above. It will be contrast = first - second.
>
> 5. Finally, once you have closed QDEC, is it possible to reopen the
> files again in the Gui? Or would you have to rerun the analysis?
sorry, not sure
>
> Thank you for help and please let me know if you need any further
> clarification.
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
------------------------------
Message: 20
Date: Thu, 6 Apr 2017 16:52:33 -0400
From: Arnaud Bor? <arnaud.bore@gmail.com>
Subject: [Freesurfer] QDEC and ROI drawing
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAPA8YjZO-wfJ1h19QZK5JNnA7G+fmXEUsQ+YjQDcC-3S9mWUXA@mail.gm >ail.com
Content-Type: text/plain; charset="utf-8"
Dear Freesurfer's experts,
I draw a specific region on fsaverage using QDEC, then I mapped this label
on each subject using mri_label2label. I looked at these registered labels
using freeview. Most of them are perfect but for some of them I would like
to correct the segmentation. I would like to modify it using QDEC but when
I overlay this label on the surface of my subject it has been shifted. I
think this shift is because QDEC is using fsaverage as the standard space.
I try opening QDEC using the "average" option and use the subject I want
but I still get this shift. am I missing something ?
Thank you in advance for your help.
Arnaud Bore
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Message: 21
Date: Thu, 6 Apr 2017 16:53:32 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] QDEC and ROI drawing
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <793cd266-aae2-0b71-638e-cb620c08a3b6@nmr.mgh.harvard.edu >
Content-Type: text/plain; charset=windows-1252; format=flowed
what is your label2label command line?
On 04/06/2017 04:52 PM, Arnaud Bor? wrote:
> Dear Freesurfer's experts,
> I draw a specific region on fsaverage using QDEC, then I mapped this
> label on each subject using mri_label2label. I looked at these
> registered labels using freeview. Most of them are perfect but for
> some of them I would like to correct the segmentation. I would like to
> modify it using QDEC but when I overlay this label on the surface of
> my subject it has been shifted. I think this shift is because QDEC is
> using fsaverage as the standard space. I try opening QDEC using the
> "average" option and use the subject I want but I still get this
> shift. am I missing something ?
> Thank you in advance for your help.
> Arnaud Bore
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
------------------------------
Message: 22
Date: Thu, 6 Apr 2017 21:08:19 +0000
From: "Lim, Lena" <lena.lim@kcl.ac.uk>
Subject: Re: [Freesurfer] QDEC-volume, thickness and area
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<HE1PR0301MB2233E43DFD8B11E3CE0A0016C20D0@HE1PR0301MB2233.eu >rprd03.prod.outlook.com
Content-Type: text/plain; charset="windows-1252"
Thanks, Doug.
There is no significant interaction and I merged the males and females within each group, but the reviewer wants me to include gender as a covariate. Do we always need to control for gender esp. when the group x gender is insignificant? Will that be "over-controlled"?
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu > on behalf of Douglas N Greve <greve@nmr.mgh.harvard.edu>
Sent: 06 April 2017 20:45
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] QDEC-volume, thickness and area
what do you mean they do not differ in gender ratio? Just that the
relative number of M/F is the same in each group? If there is not a
significant interaction between gender and group, then you can usually
merge the genders.
On 04/05/2017 05:13 PM, Lim, Lena wrote:
>
> Dear Freesurfer Experts,
>
> 1) I have 2 groups (A & B), which do not differ in terms of gender
> ratio. If there were no significant regions for Group-Gender
> interaction in mean cortical thickness in the QDEC analysis, can I
> conclude that gender does not influence the effect of group on
> thickness? The differences between A and B on mean thickness is not
> affected by Gender? Is this valid or do I need to add Gender as a
> covariate even though the group do not differ on gender ratio?
>
> 2) A reviewer pointed that it is not right to test for group
> differences in volume once I have tested for thickness and area,
> especially when there is a cluster where A and B do not differ
> significantly in thickness and area but they differ significantly in
> volume?Is this right?
>
> Please kindly advise.
>
> Many thanks,
>
> Lena
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://emea01.safelinks.protection.outlook.com/?url=https% 3A%2F%2Fmail.nmr.mgh.harvard. edu%2Fmailman%2Flistinfo% 2Ffreesurfer&data=01%7C01% 7Clena.lim%40kcl.ac.uk%7C1a7a3 062e8634c0e8d1c08d47d2577ca%7C 8370cf1416f34c16b83c7240716543 56%7C0&sdata=PhNkIdT%2Fj8FHEIG 2Wo1UjfG65ns90Ao7ajxUX7ErJus% 3D&reserved=0
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://emea01.safelinks.protection.outlook.com/?url=https% 3A%2F%2Fgate.nmr.mgh.harvard. edu%2Ffiledrop2&data=01%7C01% 7Clena.lim%40kcl.ac.uk%7C1a7a3 062e8634c0e8d1c08d47d2577ca%7C 8370cf1416f34c16b83c7240716543 56%7C0&sdata=sLX6wB91T%2FSYsH2 ihNMK39jOGhYZgcSWos3D2cfO0RE% 3D&reserved=0
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Message: 23
Date: Thu, 6 Apr 2017 17:17:04 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] QDEC-volume, thickness and area
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <989131f9-3095-bde5-437e-36794a25df65@nmr.mgh.harvard.edu >
Content-Type: text/plain; charset=windows-1252; format=flowed
probably so. It is up to you whether you want to fight the reviewer or not.
On 04/06/2017 05:08 PM, Lim, Lena wrote:
>
> Thanks, Doug.
>
>
> There is no significant interaction and I merged the males and females
> within each group, but the reviewer wants me to include gender as a
> covariate. Do we always need to control for gender esp. when the group
> x gender is insignificant? Will that be "over-controlled"?
>
>
>
> ------------------------------------------------------------ ------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu > on behalf of Douglas N Greve
> <greve@nmr.mgh.harvard.edu>
> *Sent:* 06 April 2017 20:45
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] QDEC-volume, thickness and area
> what do you mean they do not differ in gender ratio? Just that the
> relative number of M/F is the same in each group? If there is not a
> significant interaction between gender and group, then you can usually
> merge the genders.
>
>
> On 04/05/2017 05:13 PM, Lim, Lena wrote:
> >
> > Dear Freesurfer Experts,
> >
> > 1) I have 2 groups (A & B), which do not differ in terms of gender
> > ratio. If there were no significant regions for Group-Gender
> > interaction in mean cortical thickness in the QDEC analysis, can I
> > conclude that gender does not influence the effect of group on
> > thickness? The differences between A and B on mean thickness is not
> > affected by Gender? Is this valid or do I need to add Gender as a
> > covariate even though the group do not differ on gender ratio?
> >
> > 2) A reviewer pointed that it is not right to test for group
> > differences in volume once I have tested for thickness and area,
> > especially when there is a cluster where A and B do not differ
> > significantly in thickness and area but they differ significantly in
> > volume?Is this right?
> >
> > Please kindly advise.
> >
> > Many thanks,
> >
> > Lena
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> >
> https://emea01.safelinks.protection.outlook.com/?url=https% 3A%2F%2Fmail.nmr.mgh.harvard. edu%2Fmailman%2Flistinfo% 2Ffreesurfer&data=01%7C01% 7Clena.lim%40kcl.ac.uk%7C1a7a3 062e8634c0e8d1c08d47d2577ca%7C 8370cf1416f34c16b83c7240716543 56%7C0&sdata=PhNkIdT%2Fj8FHEIG 2Wo1UjfG65ns90Ao7ajxUX7ErJus% 3D&reserved=0
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop:
> https://emea01.safelinks.protection.outlook.com/?url=https% 3A%2F%2Fgate.nmr.mgh.harvard. edu%2Ffiledrop2&data=01%7C01% 7Clena.lim%40kcl.ac.uk%7C1a7a3 062e8634c0e8d1c08d47d2577ca%7C 8370cf1416f34c16b83c7240716543 56%7C0&sdata=sLX6wB91T%2FSYsH2 ihNMK39jOGhYZgcSWos3D2cfO0RE% 3D&reserved=0
> https://emea01.safelinks.protection.outlook.com/?url=www. nmr.mgh.harvard.edu%2Ffacility %2Ffiledrop%2Findex.html&data= 01%7C01%7Clena.lim%40kcl.ac. uk%7C1a7a3062e8634c0e8d1c08d47 d2577ca%7C8370cf1416f34c16b83c 724071654356%7C0&sdata=uCgDjaH FBNRCI0uSukR9fcgOVVo6Fhr5gGZIJ slPy4E%3D&reserved=0
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://emea01.safelinks.protection.outlook.com/?url=https% 3A%2F%2Fmail.nmr.mgh.harvard. edu%2Fmailman%2Flistinfo% 2Ffreesurfer&data=01%7C01% 7Clena.lim%40kcl.ac.uk%7C1a7a3 062e8634c0e8d1c08d47d2577ca%7C 8370cf1416f34c16b83c7240716543 56%7C0&sdata=PhNkIdT%2Fj8FHEIG 2Wo1UjfG65ns90Ao7ajxUX7ErJus% 3D&reserved=0
>
>
> 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
> contains patient information, please contact the Partners Compliance
> HelpLine at
> https://emea01.safelinks.protection.outlook.com/?url=http% 3A%2F%2Fwww.partners.org%2Fcom plianceline&data=01%7C01%7Clen a.lim%40kcl.ac.uk%7C1a7a3062e8 634c0e8d1c08d47d2577ca%7C8370c f1416f34c16b83c724071654356% 7C0&sdata=fCWNr93ZrBggNtOlph5y LyklpklGrCz3ZH2aREJ8WoY%3D& reserved=0
> . 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.
>
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> _______________________________________________
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
------------------------------
Message: 24
Date: Thu, 6 Apr 2017 23:26:38 +0200 (CEST)
From: <stdp82@virgilio.it>
Subject: [Freesurfer] R: Re: R: R: Re: R: Re: Whole preprocessing with
FAST without to perform a seed based analysis
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<279193799.11183291491513998781.JavaMail.httpd@fep-webmail- 07.iol.local>
Content-Type: text/plain; charset="utf-8"
Thanks.The file could not be open by fslview.I presume that it is inflated.How can I do to transform it?Stefano
----Messaggio originale----
Da: "Douglas Greve" <greve@nmr.mgh.harvard.edu>
Data: 6-apr-2017 17.56
A: <freesurfer@nmr.mgh.harvard.edu >
Ogg: Re: [Freesurfer] R: R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis
It will be in the space that you analyzed it in. If you want the
native space, then use -native when running preproc-sess and
mkanalysis
On 4/6/17 2:34 AM, stdp82@virgilio.it
wrote:
Furthermore, the res-001.nii which is produce in
produced in the res folder in not the same dimension of f.nii.
I would do the whole FAST preprocessing on f.nii.,
maintaining the same dimension and open it with FSL.
Thanks
Stefano
----Messaggio originale----
Da: stdp82@virgilio.it
Data: 5-apr-2017 23.39
A: "Freesurfer support
list"<freesurfer@nmr.mgh.harvard.edu >
Ogg: [Freesurfer] R: Re: R: Re: Whole preprocessing with FAST
without to perform a seed based analysis
Hi,
as you advise I have run selxavg3-sess with the -svres
option.
I found a folder called "res" which contain
"res-001.nii". Is it the f.nii fully processed?
Thanks
Stefano
----Messaggio originale----
Da: "Douglas Greve" <greve@nmr.mgh.harvard.edu>
Data: 14-mar-2017 17.38
A: <freesurfer@nmr.mgh.harvard.edu >
Ogg: Re: [Freesurfer] R: Re: Whole preprocessing with FAST
without to perform a seed based analysis
You can't on either occasion just using preproc-sess.
You can create an analysis with those components, then
run selxavg3-sess with the -svres option. This will
create a folder called eres with volumes that have had
all the nuisance variables and low freqeuncies regressed
out
On 3/14/17 12:32 PM, stdp82@virgilio.it
wrote:
Thanks.
1- By using only preproc-sess, how can I perform
"band pass filtering"?
2- And how can I take in account the nuisance
variables: the CSF from which the top 5 principle
components, the white matter from which the top 5
principle components, motion correction parameters
(-mcextreg), 5th order polynomial. How can I eliminate
the first 4 time points?
Regards
Stefano
----Messaggio originale----
Da: "Douglas Greve" <greve@nmr.mgh.harvard.edu>
Data: 14-mar-2017 16.14
A: <freesurfer@nmr.mgh.harvard.edu >
Ogg: Re: [Freesurfer] Whole preprocessing with FAST
without to perform a seed based analysis
just use preproc-sess
On 3/14/17 10:45 AM, stdp82@virgilio.it
wrote:
Hi list,
in FS-FAST, on rs-fMRI data, is possible to
run selxavg3-sess without -a option?
I would use whole the FS-FAST to preprocess
my data. I would include the mkanalysis-sess
step but I would not perform a seed-based
analysis.
Thanks
Stefano
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Message: 25
Date: Thu, 6 Apr 2017 17:29:20 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] R: Re: R: R: Re: R: Re: Whole preprocessing
with FAST without to perform a seed based analysis
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <46c40ef7-d760-d3da-9a07-c88ab943b1fa@nmr.mgh.harvard.edu >
Content-Type: text/plain; charset=windows-1252; format=flowed
depends on your analysis but probably so
On 04/06/2017 05:26 PM, stdp82@virgilio.it wrote:
> Thanks.
> The file could not be open by fslview.
> I presume that it is inflated.
> How can I do to transform it?
> Stefano
>
> ----Messaggio originale----
> Da: "Douglas Greve" <greve@nmr.mgh.harvard.edu>
> Data: 6-apr-2017 17.56
> A: <freesurfer@nmr.mgh.harvard.edu >
> Ogg: Re: [Freesurfer] R: R: Re: R: Re: Whole preprocessing with
> FAST without to perform a seed based analysis
>
> It will be in the space that you analyzed it in. If you want the
> native space, then use -native when running preproc-sess and
> mkanalysis
>
>
> On 4/6/17 2:34 AM, stdp82@virgilio.it wrote:
>> Furthermore, the res-001.nii which is produce in produced in the
>> res folder in not the same dimension of f.nii.
>> I would do the whole FAST preprocessing on f.nii., maintaining
>> the same dimension and open it with FSL.
>> Thanks
>> Stefano
>>
>> ----Messaggio originale----
>> Da: stdp82@virgilio.it
>> Data: 5-apr-2017 23.39
>> A: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu >
>> Ogg: [Freesurfer] R: Re: R: Re: Whole preprocessing with FAST
>> without to perform a seed based analysis
>>
>> Hi,
>>
>> as you advise I have run selxavg3-sess with the -svres option.
>> I found a folder called "res" which contain "res-001.nii". Is
>> it the f.nii fully processed?
>> Thanks
>> Stefano
>>
>> ----Messaggio originale----
>> Da: "Douglas Greve" <greve@nmr.mgh.harvard.edu>
>> Data: 14-mar-2017 17.38
>> A: <freesurfer@nmr.mgh.harvard.edu >
>> Ogg: Re: [Freesurfer] R: Re: Whole preprocessing with
>> FAST without to perform a seed based analysis
>>
>> You can't on either occasion just using preproc-sess.
>> You can create an analysis with those components, then
>> run selxavg3-sess with the -svres option. This will
>> create a folder called eres with volumes that have had
>> all the nuisance variables and low freqeuncies regressed out
>>
>>
>> On 3/14/17 12:32 PM, stdp82@virgilio.it wrote:
>>> Thanks.
>>> 1- By using only preproc-sess, how can I perform "band
>>> pass filtering"?
>>> 2- And how can I take in account the nuisance variables:
>>> the CSF from which the top 5 principle components, the
>>> white matter from which the top 5 principle components,
>>> motion correction parameters (-mcextreg), 5th order
>>> polynomial. How can I eliminate the first 4 time points?
>>> Regards
>>> Stefano
>>>
>>> ----Messaggio originale----
>>> Da: "Douglas Greve" <greve@nmr.mgh.harvard.edu>
>>> Data: 14-mar-2017 16.14
>>> A: <freesurfer@nmr.mgh.harvard.edu >
>>> Ogg: Re: [Freesurfer] Whole preprocessing with FAST
>>> without to perform a seed based analysis
>>>
>>> just use preproc-sess
>>>
>>>
>>> On 3/14/17 10:45 AM, stdp82@virgilio.it wrote:
>>>> Hi list,
>>>> in FS-FAST, on rs-fMRI data, is possible to run
>>>> selxavg3-sess without -a option?
>>>> I would use whole the FS-FAST to preprocess my
>>>> data. I would include the mkanalysis-sess step but
>>>> I would not perform a seed-based analysis.
>>>> Thanks
>>>> Stefano
>>>>
>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfe r
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfe r
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfe r
>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
------------------------------
Message: 26
Date: Thu, 6 Apr 2017 22:01:08 +0000
From: "Limachia, Gaurang (NIH/NINDS) [F]" <gaurang.limachia@nih.gov>
Subject: [Freesurfer] QDEC-Cortical Thickness
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID: <64A12700-9AC2-4072-A4AC-675A7621FB45@nih.gov >
Content-Type: text/plain; charset="utf-8"
Hello Freesurfer Experts,
I want to compare the cortical thickness between the groups (HC & Patients), and wanted to know where qdec shows this information. Once the design tab is loaded, I am seeing the question in the analysis results ? does the correlation between thickness and Age differ from zero? Do I need to a run the command for GLM in order to see if there is a cortical difference between the two populations? I would greatly appreciate your help.
Thanks,
Gaurang
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Message: 27
Date: Thu, 06 Apr 2017 22:11:47 +0000
From: Linda Zhang <lzhang87@gmail.com>
Subject: Re: [Freesurfer] Custom registration template
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<CABCBU0VuY8Lf_tnQPkFuKUk7P9DvXBo4Nc7E=29NRaZU2aykoQ@mail. gmail.com >
Content-Type: text/plain; charset="utf-8"
Hi Douglas,
Thanks, good to know! That was the full terminal output after I ran
mris_preproc, though.
Cheers,
Linda
On Thu, 6 Apr 2017 at 22:07 Douglas N Greve <greve@nmr.mgh.harvard.edu>
wrote:
> 1. The "..." means to include the other options needed for the command
> to run. Looks like you figured it out. Using -f as you have is correct.
>
> 2. can you send the full terminal output?
>
>
> On 04/06/2017 08:55 AM, Linda Zhang wrote:
> > Dear all,
> >
> > I've been following the instructions for building a custom
> > registration template as written here
> > (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTempl ) andates
> > here
> > (
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011- May/018345.html
> ).
> >
> >
> > I'm now at the mris_preproc stage and according to the instructions,
> > the command should be:
> >
> > # Get thickness values in the newtemplate space for GLM analysis
> > mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s
> > subj3 ...
> >
> > I put my subject list into a text file and replaced --s with --f
> > [subjlist] but kept everything else the same. I got two errors for no
> > source hemi specified and no output specified, so I added --hemi lh
> > and --out lh.surfreg.newtemplate.thick --meas thickness. Am I
> > supposed to do this, and will the output file be used for anything
> > else down the line, i.e., should it be named something more specific?
> > I see that the next step is to rerun the make_average_subject, but I
> > don't see where the output from the mris_preproc step would figure in.
> >
> > On a (maybe) separate issue, when I finally ran my command line:
> >
> > mris_preproc --surfreg sphere.reg.newtemplate --f subjlist --hemi lh
> > --out lh.surfreg.newtemplate.thick --meas thickness
> >
> > I got the following error:
> >
> > nsubjects=100
> > tmpdir is ./tmp.mris_preproc.25619
> > /home/fsuser/data
> > set: Variable name must contain alphanumeric characters.
> >
> > I'm not sure where the problem might be here. I'm running FreeSurfer
> > v.5.3 in Virtualbox, and I haven't had any problems while running
> > recon-all on the subjects previously.
> >
> > Any insight would be greatly appreciated, thank you!
> >
> > Cheers,
> > Linda
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
>
> _______________________________________________
> 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
> 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.
>
>
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Message: 28
Date: Thu, 6 Apr 2017 17:28:21 -0500
From: "Gullickson, James" <jgullickson02@hamline.edu>
Subject: Re: [Freesurfer] Ventricle-to-Brain Ratio
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<CAELhUFOrKPp7WrhDF0LhtXTkC2F2V+AyfoKvB58XZ3teMwXsVQ@mail.gm >ail.com
Content-Type: text/plain; charset="utf-8"
Doug,
Thanks for your reply.
Difference between the two TVV methods ranges between 1-6%
Difference between the two TBV methods ranges between 2-4%
Basically, my question is two-fold:
a) what is the most accurate representation of total ventricular volume
b) what is the most accurate representation of total brain volume (all
parenchyma)
Best,
James
On Thu, Apr 6, 2017 at 3:17 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu>
wrote:
> that looks right. how different are the values?
>
>
> On 04/05/2017 10:58 AM, Gullickson, James wrote:
> > Hello all,
> >
> > I want to calculate a Ventricle-to-Brain ratio (VBR) as a measure of
> > parenchymal atrophy using Freesurfer version 5.3.0. I have tried to go
> > about this using the aseg.stats output (using asegstats2table), but am
> > running into inconsistencies.
> >
> > The basic calculation for VBR is:
> >
> > (Total Ventricular Volume/Total Brain Volume) * 100
> >
> > i.e. Bigler, E. D. (2013). Traumatic brain injury, neuroimaging, and
> > neurodegeneration. /Frontiers in human neuroscience/, /7/, 395.
> >
> >
> > What is the best way to get Total Ventricular Volume (TVV) and Total
> > Brain Volume (TBV) for this calculation? I have tried several ways,
> > which lead to different values:
> >
> > TVV = left lateral ventricle + left inf lateral ventricle + right
> > lateral ventricle + right inf lateral ventricle + 3rd ventricle + 4th
> > ventricle + 5th ventricle + choroid plexus
> >
> > which gives me a different result than
> >
> > TVV = BrainSegVol - BrainSegVolNotVent
> >
> >
> > and for TBV
> >
> > TBV = TotalGrayVol + CorticalWhiteMatterVol
> >
> > which differs from
> >
> > TBV = BrainSegVolNotVent
> >
> >
> > Thank you for your help,
> >
> > James Gullickson
> >
> >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
>
> _______________________________________________
> 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
> 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.
>
>
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Message: 29
Date: Thu, 6 Apr 2017 23:28:02 +0000
From: Ilaria Sani <isani01@mail.rockefeller.edu>
Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID: <cdf628175a004b51adf2bc86f4a0cc5a@RUMBX12.rockefeller.edu >
Content-Type: text/plain; charset="iso-8859-7"
Hi Doug,
Thanks for the tip. I can load the volume now!
I'm getting different types of errors when I proceed with my analyses though.
Can you help me to understand why it works when data are decompressed and in what way data are different now.
Thanks a lot,
Ilaria
-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu ] On Behalf Of Douglas N Greve
Sent: Thursday, April 6, 2017 3:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
is it a compressed nifti (nii.gz)? If so, try uncompressing it first
On 04/06/2017 02:53 PM, Ilaria Sani wrote:
> Hi Bruce,
>
> Not sure this answer your question...
>
> In matlab workspace, I am able to load data in two halves:
>
> H1=MRIread(half1)
> H2=MRIread(half2)
>
> And then concatenate the volumes
> concatenate them var=cat(4,H1,H2).
>
> So, somehow matlab can handle...
>
> However, when those operations are embedded inside a function (like in the case of load_nifti and MRIread) I get the error.
>
>
> Thanks,
> Ilaria
>
>
> -----Original Message-----
> From: freesurfer-bounces@nmr.mgh.harvard.edu
> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu ] On Behalf Of Bruce
> Fischl
> Sent: Thursday, April 6, 2017 1:36 PM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
> Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
>
> Hi Ilaria
>
> do you have any reason to believe that it isn't just out of memory? If
> so, there's not much to do other than get more RAM or use a different
> machine
>
> cheers
> Bruce
>
>
> On Thu,
> 6 Apr 2017, Ilaria Sani wrote:
>
>> Dear All,
>>
>>
>>
>> I?m trying to load a pretty big diffusion MRI dataset (320x320x260x122).
>>
>> I?m running matlab 2015a 64bit on a linux machine.
>>
>>
>>
>> I?m using MRIread, which in turn calls load_nifti.
>>
>> I?m getting the following error:
>>
>>
>>
>> Error using +
>>
>> Out of memory. Type HELP MEMORY for your options.
>>
>>
>>
>> Error in load_nifti (line 158)
>>
>> hdr.vol = hdr.vol * hdr.scl_slope + hdr.scl_inter;
>>
>>
>>
>> Error in MRIread (line 158)
>>
>> hdr = load_nifti(fspec,headeronly);
>>
>>
>>
>> When I load half dataset (320x320x260x61) it works ok.
>>
>> I tried to increase the Maximum array size in Matalb (default 1,000 - now 10,000), but I?m still getting the error.
>>
>> I tried to change machine (which runs matlab 2013a on linux) and it worked fine.
>>
>>
>>
>> I think this is due to some matlab settings.
>>
>> Can anyone help?
>>
>>
>>
>> Thanks a lot,
>>
>> Ilaria
>>
>>
>>
>>
>>
>> -------------------------------------------
>> Ilaria Sani, PhD
>> Postdoctoral Fellow, Freiwald Lab
>> The Rockefeller University
>> 1230 York Ave., New York, NY 10065.
>> Phone: (212) 327 7699
>> Fax: (212) 327 7698
>> Email: isani01@rockefeller.edu
>>
>>
>>
>>
>>
> _______________________________________________
> Freesurfer mailing list
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>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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Fax: 617-726-7422
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------------------------------
Message: 30
Date: Fri, 7 Apr 2017 00:44:29 +0000
From: Chris Adamson <chris.adamson@mcri.edu.au>
Subject: Re: [Freesurfer] long mri_ca_register error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<43A4603348D2AC409B1B958EFE5C8B94029B028E3C@MITSMXMBX02V.mcr >i.edu.au
Content-Type: text/plain; charset="iso-8859-7"
Just the standard pipeline.
recon-all -s cross1 -all -bigventricles
recon-all -base cross -tp cross1 ... -all -bigventricles
recon-all -long cross1 cross -all -bigventricles
-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu ] On Behalf Of Bruce Fischl
Sent: Friday, 7 April 2017 3:37 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Subject: Re: [Freesurfer] long mri_ca_register error
Hi Chris
it's possible we never looked at -bigventricle in the long stage. What was your recon-all command line?
cheers
Bruce
On Thu, 6 Apr 2017, Chris Adamson wrote:
>
> It happens when I use -bigventricles.
>
> ?
>
> From: freesurfer-bounces@nmr.mgh.harvard.edu
> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu ] On Behalf Of Chris
> Adamson
> Sent: Thursday, 6 April 2017 12:27 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] long mri_ca_register error
>
> ?
>
> Freesurfer devs,
>
> ?
>
> In freesurfer 6 stable I?m having a problem at the careg stage of the
> long. The relevant recon-all log is pasted below. Could you point me to where to debug this problem?
>
> ?
>
> Cheers,
>
> ?
>
> Chris.
>
> ?
>
> mri_ca_register -rusage
> 136_S_0426_20070604.long.136_S_0426/touch/rusage.mri_ca_regi ster.dat
> -bigventricles -smoothness 0.5 -levels 2 -A 1 -l
> *base*/transforms/talairach.m3z identity.nofile -align-after -mask
> brainmask.mgz norm.mgz
> /usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700. gca
> transforms/talairach.m3z
>
> ?
>
> handling expanded ventricles...
>
> l_smoothness = 0.50
>
> levels = 2
>
> smoothing gradient with 1 averages...
>
> reading previously computed atlas xform
> /isilon/data/addo/ADNI3T/freesurfer6/136_S_0426/mri/transfor ms/talaira
> ch.m3z and applying inverse registration identity.nofile
>
> renormalizing sequences with structure alignment, equivalent to:
>
> ??? -renormalize
>
> ??? -regularize_mean 0.500
>
> ??? -regularize 0.500
>
> using MR volume brainmask.mgz to mask input volume...
>
> ?
>
> == Number of threads available to mri_ca_register for OpenMP = 2 ==
>
> reading 1 input volumes...
>
> logging results to talairach.log
>
> reading input volume 'norm.mgz'...
>
> reading GCA '/usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700 .gca'...
>
> label assignment complete, 0 changed (0.00%)
>
> TransformSample: gcam has not been inverted!
>
> freeing gibbs priors...done.
>
> average std[0] = 5.0
>
> setting orig areas to linear transform determinant scaled 8.40
>
> writing talairach.invalid.mgz
>
> writing talairach.status.mgz
>
> registering ventricular system...
>
> using threshold 45.0 from atlas ventricle (20.1 +- 5.0) and caudate
> (70.0 +- 5.0) distributions for initial ventricular estimate
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> TransformSample: gcam has not been inverted!
>
> No such file or directory
>
> ?
>
> Dr Chris Adamson
>
> Senior Research Officer
>
> Developmental Imaging, Clinical Sciences
>
> ?
>
> Murdoch Childrens Research Institute
>
> The Royal Children?s Hospital
>
> Flemington Road, Parkville, VIC 3052 Australia
>
> E?chris.adamson@mcri.edu.au
>
> www.mcri.edu.au
>
> ?
>
> ?
>
> This e-mail and any attachments to it (the "Communication") are,
> unless otherwise stated, confidential, may contain copyright material
> and is for the use only of the intended recipient. If you receive the
> Communication in error, please notify the sender immediately by return
> e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.
>
> ?
>
> P?Please consider the environment before?printing this email
>
> ?
>
>
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------------------------------
Message: 31
Date: Fri, 7 Apr 2017 10:23:03 +0530
From: Dilip Puri <dilippuripuri@gmail.com>
Subject: Re: [Freesurfer] help
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<CAHLUP+B3v_roRUCZjA+OJM+4krJNfVQO3HcVXgq9bY-R0Mq_zg@mail. >gmail.com
Content-Type: text/plain; charset="utf-8"
Hi everyone,
when I used following command:
mri_binarize --i myfile.img --match 17 --binval -1 --o your.lefthippo.nii.gz
then I got output your.lefthippo.nii.gz file when I read this file using
FREEVIEW then it completly different from original mask.
Thanks
Dilip?
On Thu, Apr 6, 2017 at 11:08 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
> Hi Dilip
>
> yes, freesurfer will do this for you, although the labels will be 17 for
> left hippocampus and 53 for right.
>
> cheers
> Bruce
> On Thu, 6 Apr 2017, Dilip Puri wrote:
>
> > Hi everyone,
> >
> > I am working on Hippocampus segmentation using Neural Networks for that
> I need labeled images of Hippocampus corresponding to original images.
> >
> > I am using OASIS Dataset for this. I want to generate labeled images
> using FREESURFER. Is there any way to label each 3D co-ordinate
> > HippoCampus -1
> > Otherwise - 0
> >
> > Here are sample files link
> >
> > Kindly help me!
> >
> >
> > Dilip Puri
> > IIIT Vadodara
> >
> >
> _______________________________________________
> 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
> 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.
>
>
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------------------------------
Message: 32
Date: Fri, 7 Apr 2017 09:52:53 +0100
From: Shane S <shane.schofield@yahoo.com>
Subject: [Freesurfer] How to segment subnuclei of thalamus?
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID: <etPan.58e75365.225461f5.17c60@yahoo.com >
Content-Type: text/plain; charset="utf-8"
Hello Experts,
I am interested to do a segmentation of the thalamus subnuclei based on T1 data. Is there any atlas that I could use for this??
Best Wishes,
S
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------------------------------
Message: 33
Date: Fri, 07 Apr 2017 18:41:48 +0900
From: kjunji@med.kanazawa-u.ac.jp
Subject: [Freesurfer] withdrawing from the mailing list.
To: Freesurfer@nmr.mgh.harvard.edu
Message-ID: <3a1b2370509f7f0adb8d1b5ff38a7154@med.kanazawa-u.ac.jp >
Content-Type: text/plain; charset=US-ASCII; format=flowed
Dear Secretariat of Freesurfer mailing list
I want to stop receiving emails from the Freesurfer mailing list.
Please teach me to withdraw from the mailing list.
Sincerely yours.
Junji Komatsu in Kanazawa university hospital.
------------------------------
Message: 34
Date: Fri, 7 Apr 2017 12:48:36 +0200
From: Yong Li <yongli86@gmail.com>
Subject: Re: [Freesurfer] QA Tools v1.2 and future release
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAKmw9f=zG4G-DDuRpuochiyn91w9YAx8e1L-r5+=_a9heyTUmQ@mail. gmail.com >
Content-Type: text/plain; charset="utf-8"
Dear Freesurfer Experts,
Please excuse my long email yesterday.
Now, I finished code update of the outlier detection part for brainstem
substructures (bs) and Hippocampal Subfields (hc) modules. Code updated in
the similar way as my last email except that I combined the output of both
modules to simplify the process. The following log files might show some
clue of my exploration:
YongbshcLUT (like asegLUT_112511):
Medulla 0.287988 +/- 0.0304379
Pons 0.864817 +/- 0.128019
SCP 0.0161611 +/- 0.0030778
Midbrain 0.388938 +/- 0.038842
Whole_brainstem 1.8246 +/- 0.184472
Left-Hippocampal_tail 0.0291617 +/- 0.00437039
Left-subiculum 0.0237801 +/- 0.0044348
Left-CA1 0.0387709 +/- 0.00612168
Left-hippocampal-fissure 0.00944849 +/- 0.00188347
Left-presubiculum 0.0177329 +/- 0.00272706
Left-parasubiculum 0.00372024 +/- 0.000876862
Left-molecular_layer_HP 0.0320802 +/- 0.00806223
Left-GC-ML-DG 0.0186971 +/- 0.00308382
Left-CA3 0.0120106 +/- 0.00198279
Left-CA4 0.0132618 +/- 0.00261687
Left-fimbria 0.00371701 +/- 0.00166146
Left-HATA 0.0031189 +/- 0.000692806
Left-Whole_hippocampus 0.190022 +/- 0.0246413
Right-Hippocampal_tail 0.030817 +/- 0.00496078
Right-subiculum 0.0248689 +/- 0.00427691
Right-CA1 0.0370719 +/- 0.00873442
Right-hippocampal-fissure 0.0103329 +/- 0.00187117
Right-presubiculum 0.0178487 +/- 0.00260947
Right-parasubiculum 0.00380418 +/- 0.000861778
Right-molecular_layer_HP 0.032938 +/- 0.00448073
Right-GC-ML-DG 0.0168729 +/- 0.00304788
Right-CA3 0.0130893 +/- 0.00239818
Right-CA4 0.0143492 +/- 0.00281808
Right-fimbria 0.00438099 +/- 0.00176098
Right-HATA 0.00338842 +/- 0.0006037
Right-Whole_hippocampus 0.198797 +/- 0.0243668
an example subject's bshc.stats (like aseg.stats):
Medulla 4288.386728
Pons 12836.783824
SCP 194.446727
Midbrain 8306.988464
Whole_brainstem 22293.878740
Left-Hippocampal_tail 462.086606
Left-subiculum 307.970217
Left-CA1 816.878818
Left-hippocampal-fissure 118.986208
Left-presubiculum 227.392060
Left-parasubiculum 84.381831
Left-molecular_layer_HP 841.496111
Left-GC-ML-DG 238.308049
Left-CA3 183.383724
Left-CA4 196.098618
Left-fimbria 73.990998
Left-HATA 36.237082
Left-Whole_hippocampus 2838.187477
Right-Hippocampal_tail 408.832729
Right-subiculum 388.667888
Right-CA1 801.601831
Right-hippocampal-fissure 132.071091
Right-presubiculum 242.179137
Right-parasubiculum 43.414171
Right-molecular_layer_HP 487.298072
Right-GC-ML-DG 246.283617
Right-CA3 164.849646
Right-CA4 209.108368
Right-fimbria 90.291400
Right-HATA 42.073898
Right-Whole_hippocampus 2791.300419
icv.txt (actually eITV instead of ICV):
1420463.178113
bshc_outliers.log:
Subject 008 Right-HATA value .002080900 is an outlier ...
Note: all data here are kind of simulation results because of data safety
reason and these logs only serve as signs of correct code update.
I guess that both the only output of bs and hc (bshc.stats) is segment
volume, not the 'normMean normStdDev ...' in aseg.stats.
So is it senseful to include those 'norm*' measures in the bs & hc modules
in the future?
BTW, is there an advantage to use normMax / eITV rather than normMean /
eITV in outlier detection in theory?
Thank you very much again!
I wish all of you a nice weekend!
Best regards,
Yong
_________________________
Yong Li, PhD
Department of Neurology,
Klinikum rechts der Isar,
Technische Universit?t M?nchen,
Munich, Germany
On Thu, Apr 6, 2017 at 11:36 AM, Yong Li <yongli86@gmail.com> wrote:
> Dear Freesurfer Experts,
>
> As one of the new freesurfers, I really appreciate the excellent work of
> authors as well as great support of users' forum.
>
> A good guess of mine is that authors, e.g., Vasanth or Louis etc., are
> busy updating QA tools after the FSv6 release since the QA Tools v1.2 was
> written for FSv5.3. If so, is it possible to provide an estimated release
> date please so as to adjust my plan? Thanks for understanding!
>
> In case, it might take a while to release the next QA Tool, may I dare to
> provide my attempts of code updating of some functions in QA Tools? The
> following are the brief list of code adapting steps:
> 1. modified codes for generating file order list in recon_checker;
> 2. modified codes for matching segment names for instance from
> DefaultAsegMeans.txt in gparcmean_from_table;
> 3. adapted default_FOF and default_status_log for FSv6.
>
> After these adaptation, QA Tools ran through and I only encountered some
> 'syntax error' in terminal for 2 segments, 5th-Ventricle and
> WM-hypointensities, that I have to ask the experts to guide me through this
> point if it's of your interests. To ensure the QA Tools functioning well, I
> tested 116 elderly patients and detected reasonable outliers per patient.
> Therefore, I would like to double that my code updating based on my general
> understanding of QA Tool still fit to the basic purpose of authors by
> asking the following theoretical questions:
>
> 1. SNR and segments outliers detection are measures of quality assessment
> in QA Tools. Have other factors such as subject's motion, image bias,
> resolution etc. been considered in QA Tools or future release? The default
> SNR threshold is 16 based on any reference? The max SNR of my patients so
> far is 32. Any idea of scores of healthy elderly controls?
>
> 2. The QA Tools v1.2 analyzes aseg.stats output. Is it possible to include
> output of brainstem substructures and HippocampalSubfields of FSv6? If yes,
> I would like to adapt the codes and provide you some feedback if you think
> that I can help bit.
>
> 3. Future directions mentioned in QA Tools wiki site are interesting and
> thoughtful. Are other features like 'Detect outliers in aparc and aparc2009
> volumes' on the way?
>
> 4. Is there a function to summarize all QA measures to csv files, like the
> quantifyBrainstemStructures.sh in brainstem substructures?
>
> Thank you in advance!
>
> Kind regards,
>
> Yong Li, PhD
> _________________________
> Department of Neurology,
> Klinikum rechts der Isar,
> Technische Universit?t M?nchen,
> Munich, Germany
>
>
>
>
>
>
>
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------------------------------
Message: 35
Date: Fri, 7 Apr 2017 11:17:20 +0000
From: Nina Jacobsen <njacob12@student.aau.dk>
Subject: [Freesurfer] Hippocampal subfield segmentation, file content
To: "freesurfer@nmr.mgh.harvard.edu " <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<C81DC33B38A91045AE898B7F15429E970125EC8B5B@AD-EXCHMBX4-1.aa >u.dk
Content-Type: text/plain; charset="iso-8859-1"
Hi All,
I have made a hippocampal subfield segmentation using FreeSurfer version 6.0 with multispectral segmentation settings, and have both labels for the right and left hippocampus. The segmentations look very nice when viewed with freeview, so all good.
Now, my problem is the file content. I would like a segmentation file, which labels all subfields with a single value (all voxels in CA1 would for example be with value 1, all voxels in CA2 would be with value 2 and so on). Does anyone know how i can gain this file? Is it in some way possible to convert the label files (lh.hippoSfLabel.v10.mgz) into such a "simple" segmentation file? Currently, the content of the label files (lh.hippoSfLabel.v10.mgz) is values in the range 0-226, which I guess origin from the RGB encoding - I opened the file with matlab.
Hope my question is clear.
Thanks,
Nina Jacobsen.
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Message: 36
Date: Fri, 7 Apr 2017 11:29:14 +0000 (UTC)
From: teodora petrova <teddi_petrova@yahoo.com>
Subject: Re: [Freesurfer] Multiple Comparisons Correction thresh error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID: <1890557955.1725598.1491564554325@mail.yahoo.com >
Content-Type: text/plain; charset="utf-8"
Hi,
We managed to avoid getting the error by typing the following in the terminal before the command:
export LC_NUMERIC="en_US.UTF-8"
Best,Teodora
On Thursday, April 6, 2017, 5:59:05 PM GMT+2, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:
I think this is a "language" problem in that it is converting the "1.3" into "1,3" and then getting confused. I'm not sure how to fix it, but I think it has to do with the LOCAL setting.
On 4/6/17 5:07 AM, teodora petrova wrote:
Hello,
I would like to correct my glm_fit results for multiple comparisons.? I am using the following commands, similar to the one in the group analysis tutorial:
mri_glmfit-sim? --glmdir lh.index.glmdir? --cache 1.3 abs? --cwp 0.05? --2spaces mri_glmfit-sim? --glmdir lh.index.glmdir? --cache 2.0 pos? --cwp 0.05? --2spaces
And receive the following errors:
ERROR:thresh=1,3, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 ERROR:thresh=2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
I am sure I am typing a point, but it is read as a comma. Any ideas why?
Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Platform: Ubuntu MATE 16.04 Thank you very much!
Regards, Teodora
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Message: 37
Date: Fri, 7 Apr 2017 12:34:37 +0100
From: Arman Eshaghi <arman.eshaghi@gmail.com>
Subject: [Freesurfer] Longitudinal Pipeline
To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<CAKy1A=HxDhEY92goc3-UsLGABx9k0=AY4hCV_2+QsQV3goXCGA@mail. gmail.com >
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Hi,
I wonder if there is a way for mri_robust_template to perform iterative
registration with 9 DOF rather than 6-7 default. The rational is to allow
for a bit of scaling to adjust for potential scanner drifts in a
longitudinal study over years.
Thanks,
Arman
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Message: 38
Date: Fri, 7 Apr 2017 12:42:34 +0000
From: "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.uk>
Subject: Re: [Freesurfer] Hippocampal subfield segmentation, file
content
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID: <B9A34CC0-D6BB-4AEE-9428-7E715598727E@ucl.ac.uk >
Content-Type: text/plain; charset="utf-8"
Hi Nina,
I?m very glad to hear that the segmentations look satisfactory :-)
The ?h.hippoSfLabel.v10.mgz files already have that information; they are label volumes (FreeView assigns colors to the labels for visualization). The lookup table can be found in $FREESURFER_HOME/FreeSurferColorLUT.txt (you?re interested in the range 200-226).
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 7 Apr 2017, at 12:17, Nina Jacobsen <njacob12@student.aau.dk<mailto:njacob12@student.aau.dk>> wrote:
Hi All,
I have made a hippocampal subfield segmentation using FreeSurfer version 6.0 with multispectral segmentation settings, and have both labels for the right and left hippocampus. The segmentations look very nice when viewed with freeview, so all good.
Now, my problem is the file content. I would like a segmentation file, which labels all subfields with a single value (all voxels in CA1 would for example be with value 1, all voxels in CA2 would be with value 2 and so on). Does anyone know how i can gain this file? Is it in some way possible to convert the label files (lh.hippoSfLabel.v10.mgz) into such a "simple" segmentation file? Currently, the content of the label files (lh.hippoSfLabel.v10.mgz) is values in the range 0-226, which I guess origin from the RGB encoding - I opened the file with matlab.
Hope my question is clear.
Thanks,
Nina Jacobsen.
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Message: 39
Date: Fri, 7 Apr 2017 10:27:57 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to segment subnuclei of thalamus?
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<alpine.LRH.2.20.1704071027520.23501@door.nmr.mgh.harvard. >edu
Content-Type: text/plain; charset="utf-8"
sorry, not yet. We are working on it
Bruce
On Fri, 7 Apr 2017, Shane S wrote:
> Hello Experts,
>
> I am interested to do a segmentation of the thalamus subnuclei based on T1
> data. Is there any atlas that I could use for this??
>
> Best Wishes,
> S
>
>
>
------------------------------
Message: 40
Date: Fri, 7 Apr 2017 11:11:46 -0400
From: Marissa Pifer <marissapifer@gmail.com>
Subject: [Freesurfer] Analyzing xhemi results
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<CAEHKf7bbt_mF0rH3Zynp+B25FA=7n6YnYr-_6uyO3iUA+bw=6A@mail.gm ail.com >
Content-Type: text/plain; charset="utf-8"
Hi free surfers,
I have run the xhemi process on the subjects for my study. The study is on
stroke patients and their lesions are a mix of left and right hemispheres.
In analyzing the results, we want to look at correlations between fmri
activation in M1 and the cortical thickness of M1 ipsilesional and
contralesional. To do so, I followed instructions written out in response
to a question about xhemi on the mailing list:
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-D ecember/026823.html
My question, is there a way when running the analysis step:
*# Analyze
*>* mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir
*>* glm.lh.lh-rh.thickness.sm05 \
*>* --osgm --surf fsaverage_sym lh
*>
Can I modify this command line to include my fmri data and run that
correlation also?
Thank you,
Marissa
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Message: 41
Date: Fri, 7 Apr 2017 11:47:56 -0400
From: Arnaud Bor? <arnaud.bore@gmail.com>
Subject: Re: [Freesurfer] QDEC and ROI drawing
To: freesurfer@nmr.mgh.harvard.edu, greve@nmr.mgh.harvard.edu
Message-ID:
<CAPA8YjZCsVwy0nfueXpObz45HkyCBkoaoRB8jOwXcycCyuA5AA@mail.gm >ail.com
Content-Type: text/plain; charset="utf-8"
I used this command line: mri_label2label --srclabel rh.M1_v4.label
--srcsubject fsaverage --trgsubject O_Nap_04MB --trglabel rh.M1_v4.label
--regmethod surface --hemi rh
The output label overlaps the surface using freeview but using qdec it is
shifted.
Thank you for your help.
Arnaud
2017-04-07 10:23 GMT-04:00 basile pinsard <basile.pinsard@gmail.com>:
>
> ---------- Forwarded message ----------
> From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
> Date: Thu, Apr 6, 2017 at 4:53 PM
> Subject: Re: [Freesurfer] QDEC and ROI drawing
> To: freesurfer@nmr.mgh.harvard.edu
>
>
> what is your label2label command line?
>
>
>
> On 04/06/2017 04:52 PM, Arnaud Bor? wrote:
> > Dear Freesurfer's experts,
> > I draw a specific region on fsaverage using QDEC, then I mapped this
> > label on each subject using mri_label2label. I looked at these
> > registered labels using freeview. Most of them are perfect but for
> > some of them I would like to correct the segmentation. I would like to
> > modify it using QDEC but when I overlay this label on the surface of
> > my subject it has been shifted. I think this shift is because QDEC is
> > using fsaverage as the standard space. I try opening QDEC using the
> > "average" option and use the subject I want but I still get this
> > shift. am I missing something ?
> > Thank you in advance for your help.
> > Arnaud Bore
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
>
> _______________________________________________
> 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
> 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.
>
>
>
>
> --
> Basile Pinsard
>
> *PhD candidate, *
> Laboratoire d'Imagerie Biom?dicale, UMR S 1146 / UMR 7371, Sorbonne
> Universit?s, UPMC, INSERM, CNRS
> *Brain-Cognition-Behaviour Doctoral School **, *ED3C*, *UPMC, Sorbonne
> Universit?s
> Biomedical Sciences Doctoral School, Faculty of Medicine, Universit? de
> Montr?al
> CRIUGM, Universit? de Montr?al
>
--
Arnaud BORE
Research assistant
Cellulaire : (001) 514-647-8649
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