hello experts! my name is areum. i have some question to you. i have never seen before these NIFTI format(fig.1.png) I want to see these data subjects's cortical thickness using qdec. how can i to do? plz answer me
2015-12-25 2:16 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi A-reum
you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce
On Thu, 24 Dec 2015, A-reum Min wrote:
hello experts!my name is areum.
i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me
2015-11-10 7:49 GMT+09:00 A-reum Min naniyaah@gmail.com: Hello experts! I have some question to you..
I don't need to show up so small blue regions(fig.1 blue region)
How can i control these?
2015-11-10 7:41 GMT+09:00 Douglas N Greve greve@nmr.mgh.harvard.edu: Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate.
On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... > #-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... > #----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > --average 1 --template > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/00 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.tx t > --subsample 200 --lta >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta > > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > as > movable/source volume. > --mov: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > ) > to TP 1 ( >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > > - Max Resolution used: 3 > -- gpS ( 64 , 64 , 52 ) > -- gpT ( 64 , 64 , 52 ) > - running loop to estimate saturation parameter: > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Killed > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s sub002 exited with ERRORS at Thu Nov 5 > 02:37:57 PST 2015 > > For more details, see the log file >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > 2015-10-19 11:05 GMT+09:00 A-reum Min <naniyaah@gmail.com
<mailto:naniyaah@gmail.com>>: hello experts. i have a question to you.. i'm doing recon-all stage, but errors show up likethis
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 templatecomputation.
--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 (noiterations)!
--iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling andoutput results
--subsample: Will subsample if size is larger than200 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) mmsize
and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mmsize and
(512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mmsize
and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mmsize 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 saturationparameter:
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 1for 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 SATiteratively!
i --satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 astarget for
initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everythingto init TP!
--fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output onlyfirst
template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableingintensity scaling!
--iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will performintensity
scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsample: Will subsampleif size
is larger than 200 on all axes! --subsample:: Too many arguments. [areum@localhost 14]# --lta: Will output LTAtransforms
--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 usingcubic 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 usingcubic 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 toestimate 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 04:27:16UTC 2014
x86_64 x86_64 x86_64 GNU/Linux Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exitedwith
ERRORS at Sat Oct 17 07:50:15 PDT 2015 a ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 1707:50:15 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 Oct17
08:35:33 PDT 2015 For more details, see the log file To report a problem, seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
[areum@localhost 14]# [areum@localhost 14]# For more details, see thelog file
/usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log
For: Command not found. [areum@localhost 14]# To report a problem, seehttp://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,v1.179.2.7
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, checkingfor dicoms
Found: Command not found. [areum@localhost 14]# Found 244 dicom files inseries.
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 21:55:16mreuter
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,v1.179.2.7
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, checkingfor 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 1708:09:23
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: Commandnot 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 1for template
computation. --average:: Too many arguments. [areum@localhost 14]# --template --template: Command not found. [areum@localhost 14]# --satit: Will estimate SATiteratively!
--satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 astarget for
initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everythingto init TP!
--fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output onlyfirst
template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableingintensity scaling!
--iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will performintensity
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 usingcubic 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 usingcubic 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 toestimate
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.localdomain2.6.32
Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exitedwith
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 Oct17
08:35:53 PDT 2015 For more details, see the log file To report a problem, seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
how can i to do? plz help me.. 2015-10-18 0:11 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum can you please follow the bug-reportingprocedures 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 moreuseful, but in
addition we need a lot of other informationif 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 errorsshowed up
(fig.1) how can i to do? plz, help me 2015-09-16 23:56 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: don't use .hdr. When you have a.hdr/.img
pair, just use the .img file. On 9/16/15 10:51 AM, A-reum Min wrote: hello, experts I have some question. I want to use analyze format instead ofDICOM 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.localdomain2.6.32-504.el6.x86_64 #1
SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64GNU/Linux
recon-all -s han001 exited with ERRORS atWed 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, seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
How can i to do using analyze format? 2015-08-27 23:55 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: Specify something for --seg. It justneeds to
be a surface overlay of the same size as the input. On 08/27/2015 01:49 AM, A-reum Minwrote:
> Hello doug > > i enter the ' mri_segstats --i y.mgh--vox
33 0 0 --avgwf out.dat' > then, error occured --> ERROR: mustspecify
a segmentation volume > > > 2015-08-27 12:50 GMT+09:00 DouglasGreve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: > > don't use "vertexno", just putthe
vertex number, eg, --vox 33 0 0 > > > On 8/26/15 9:22 PM, A-reum Minwrote:
>> Hello developer, >> >> I have some question to you. >> >> How can i get the significant
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
