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