Hi,
I have just installed Freesurfer and I am now following the steps in
the preprocessing tutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/
FsFastTutorial) but for some reason preproc-sess is not generating
(1) the motion corrected & smoothed volume fmcsm5.nii, and (2) the
brain mask masks/brain.nii volume, as it should.
Inspecting the terminal output, I couldn't see any potential source
of problems apart from a warning generated by Matlab which says:
Warning: Duplicate directory name: /Users/eiji/matlab.
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Warning: Executing startup failed in matlabrc.
This indicates a potentially serious problem in your MATLAB setup,
which should be resolved as soon as possible. Error detected was:
MATLAB:UndefinedFunction
Undefined command/function 'setenv'.
> In matlabrc at 224
>> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
------------------------------------------
In spite of that, preproc-sess seems to exit without errors, later
displaying 'spatiallysmooth-sess Done' and 'mkbrainmask-sess done'.
So it looks that technically there wasn't an error?
Checking the mailing lists archives, I found a recent thread
discussing a similar problem but it is not very clear to me how it
was solved in the end (Balaji? Doug?). Directory permissions looks
fine (755). Could anyone help?
(Link to the thread: http://www.mail-archive.com/
freesurfer@nmr.mgh.harvard.edu/msg07826.html. I am using the same
subject line in this post...)
I am attaching as a text file the terminal output of the command I am
executing (' preproc-sess -s mgh-101.1 -fwhm 5 ' ). I also installed
AFNI and FSL as I tried to advance in the tutorial.
This is surely not a bug report, but for the record the description
of my platform is as follows:
---------------------------------------------------------------------
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v4.0.5
Kernel info: Darwin 8.11.0 Power Macintosh
---------------------------------------------------------------------
Please include the following additional information in your report:
1) subject name -> mgh-101.1 (I suppose)
2) the entire command-line executed -> preproc-sess -s mgh-101.1 -
fwhm 5
3) the error message generated -> No obvious error message, but
fmcsm5.nii and masks/brain.nii are not generated
4) optionally include the subject's /script/recon-all.log -> (OK,
now you got me, I see there are several recon-all.log's but none in
the vicinity of the preproc tutorial directory...)
----
Any help will be greatly appreciated! If there is anything unclear,
please, let me know.
Thank you very much in advance.
Eiji
[cerezo:tutorial_subjs/fsfast-tutorial/my-study] eiji% preproc-sess -s
mgh-101.1 -fwhm 5
--------------------------------------------------------------
preproc-sess logfile is log/preproc-sess.log
--------------------------------------------------------------
instem f
mc 1 f fmc
stc 0 fmc
sm 1 fmc fmcsm5
mask 1 brain
mgh-101.1 MC -----------------------------
Mon Aug 25 15:30:40 JST 2008
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study
mc-sess -fstem f -fmcstem fmc -s mgh-101.1 -d
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study
-fsd bold -new -update -no-inorm
----------------------------------------
Logfile is
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/log/mc-mgh-101.1-bold.log
-------------------------------------------
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1
RunList: 003 005 007 010
Targ Stem is 003/f
------- ************************** -----------
------- Motion Correcting Run 003 -----------
------- ************************** -----------
sess = mgh-101.1
Mon Aug 25 15:30:43 JST 2008
mc-afni2 --i 003/f.nii --t 003/f.nii --frame 0 --o 003/fmc.nii --mcdat
003/fmc.mcdat
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
mri_info --nframes --o /tmp/mriinfo.1499 003/f.nii
log file is 003/fmc.nii.mclog
mcdat file is 003/fmc.mcdat
tmp dir is 003/tmp.mc-afni2.1499
[EMAIL PROTECTED] --------------------------------
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
mri_convert 003/f.nii 003/tmp.mc-afni2.1499/tempvol.nii.gz --nskip 0 --ndrop 84
-odt float
mri_convert 003/f.nii 003/tmp.mc-afni2.1499/tempvol.nii.gz --nskip 0 --ndrop 84
-odt float
nskip = 0
ndrop = 84
$Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $
reading from 003/f.nii...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.9973, -0.0712038, 0.0179835)
j_ras = (0.0625429, -0.951817, -0.300222)
k_ras = (0.038494, -0.298286, 0.9537)
changing data type from 4 to 3 (noscale = 0)...
Dropping last 84 frames
writing to 003/tmp.mc-afni2.1499/tempvol.nii.gz...
[EMAIL PROTECTED] --------------------------------
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
mri_convert 003/f.nii 003/tmp.mc-afni2.1499/invol.nii.gz -odt float
mri_convert 003/f.nii 003/tmp.mc-afni2.1499/invol.nii.gz -odt float
$Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $
reading from 003/f.nii...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.9973, -0.0712038, 0.0179835)
j_ras = (0.0625429, -0.951817, -0.300222)
k_ras = (0.038494, -0.298286, 0.9537)
changing data type from 4 to 3 (noscale = 0)...
writing to 003/tmp.mc-afni2.1499/invol.nii.gz...
[EMAIL PROTECTED] --------------------------------
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
3dvolreg -verbose -dfile 003/fmc.mcdat -base
003/tmp.mc-afni2.1499/tempvol.nii.gz -prefix
003/tmp.mc-afni2.1499/outvol.nii.gz 003/tmp.mc-afni2.1499/invol.nii.gz
++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Aug 21 2008) [32-bit]
++ Authored by: RW Cox
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as 003/tmp.mc-afni2.1499/tempvol.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:003/tmp.mc-afni2.1499/tempvol.nii.gz is 17.858484 degrees
from plumb.
++ Reading in base dataset 003/tmp.mc-afni2.1499/tempvol.nii.gz
++ Oblique dataset:003/tmp.mc-afni2.1499/invol.nii.gz is 17.858484 degrees from
plumb.
++ Reading input dataset 003/tmp.mc-afni2.1499/invol.nii.gz
++ Edging: x=3 y=3 z=2
++ Creating mask for -maxdisp
+ Automask has 35321 voxels
+ 5274 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 85 sub-bricks:
0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..
++ CPU time for realignment=3.78 s [=0.0445 s/sub-brick]
++ Min : roll=-0.058 pitch=-0.007 yaw=-0.048 dS=-0.054 dL=-0.105 dP=-0.106
++ Mean: roll=-0.007 pitch=+0.094 yaw=-0.023 dS=+0.145 dL=-0.029 dP=-0.026
++ Max : roll=+0.062 pitch=+0.333 yaw=+0.016 dS=+0.318 dL=+0.121 dP=+0.017
++ Max displacements (mm) for each sub-brick:
0.00 0.06 0.04 0.06 0.08 0.11 0.16 0.15 0.17 0.14 0.23 0.32 0.38 0.44 0.25
0.28 0.37 0.37 0.39 0.28 0.30 0.58 0.18 0.31 0.29 0.29 0.27 0.26 0.25 0.30 0.29
0.27 0.64 0.31 0.17 0.22 0.30 0.31 0.33 0.38 0.38 0.35 0.17 0.17 0.35 0.41 0.39
0.36 0.36 0.41 0.39 0.39 0.39 0.46 0.36 0.42 0.40 0.39 0.38 0.39 0.38 0.41 0.38
0.30 0.33 0.36 0.35 0.37 0.38 0.38 0.39 0.38 0.38 0.38 0.37 0.36 0.34 0.35 0.33
0.34 0.34 0.37 0.36 0.37 0.33
++ Max displacement in automask = 0.64 (mm) at sub-brick 32
++ Wrote dataset to disk in 003/tmp.mc-afni2.1499/outvol.nii.gz
[EMAIL PROTECTED] --------------------------------
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
mri_convert 003/tmp.mc-afni2.1499/outvol.nii.gz 003/fmc.nii --in_like 003/f.nii
mri_convert 003/tmp.mc-afni2.1499/outvol.nii.gz 003/fmc.nii --in_like 003/f.nii
reading info from 003/f.nii...
$Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $
reading from 003/tmp.mc-afni2.1499/outvol.nii.gz...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.9973, -0.0712038, 0.0179835)
j_ras = (0.0625429, -0.951817, -0.300222)
k_ras = (0.038494, -0.298286, 0.9537)
writing to 003/fmc.nii...
... cleaning up ....
Mon Aug 25 15:31:34 JST 2008
mc-afni2 done
INFO: Making external regressor from mc params
mcparams2extreg -mcfile 003/fmc.mcdat -northog 6 -extreg 003/mcextreg
Logfile is 003/mcparams2extreg.log
----------- Matlab file --------------
mcfile = '003/fmc.mcdat';
extreg = '003/mcextreg';
nkeep = [];
northog = [6];
pctorthog = [];
monly = 0;
mc = textread(mcfile);
mc = mc(:,2:7);
ntrs = size(mc,1);
if(ntrs < 6)
fprintf('ERROR: ntrs = %d < 6\n',ntrs);
if(~monly)
fprintf('Quiting matlab\n');
quit;
fprintf('should not be here\n');
end
end
if(~isempty(nkeep))
x = mc(:,1:nkeep);
elseif(~isempty(northog))
[u s v] = svd(mc);
ds = diag(s);
pct = 100*cumsum(ds)/sum(ds);
x = u(:,1:northog);
nkeep = northog;
fprintf('INFO: northog = %d, pct = %g\n',northog,pct(nkeep));
else
[u s v] = svd(mc);
ds = diag(s);
pct = 100*cumsum(ds)/sum(ds);
nkeep = min(find(pct > pctorthog));
x = u(:,1:nkeep);
fprintf('INFO: pctorthog = %g, nkeep = %d\n',pctorthog,nkeep);
end
x2 = zeros(1,1,nkeep,ntrs);
x2(1,1,:,:) = x'; %'
%fmri_svbvolume(x2,extreg);
mri.vol = permute(x2,[1 3 2 4]);
mri.tr = 0;
mri.flip_angle = 0;
mri.te = 0;
mri.ti = 0;
mri.vox2ras0 = eye(4);
mri.xsize = 1;
mri.ysize = 1;
mri.zsize = 1;
mri.volres = [1 1 1];
mri.volsize = [size(mri.vol,1) size(mri.vol,2) size(mri.vol,3)];
fname = sprintf('%s.bhdr',extreg);
MRIwrite(mri,fname);
quit;
-----------------------------------
------------------------------------------
------- matlab output --------------------
Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.
Warning:
MATLAB is starting without a display, using internal event queue.
You will not be able to display graphics on the screen.
< M A T L A B >
Copyright 1984-2005 The MathWorks, Inc.
Version 7.1.0.183 (R14) Service Pack 3
August 02, 2005
Warning: Duplicate directory name: /Users/eiji/matlab.
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Warning: Executing startup failed in matlabrc.
This indicates a potentially serious problem in your MATLAB setup,
which should be resolved as soon as possible. Error detected was:
MATLAB:UndefinedFunction
Undefined command/function 'setenv'.
> In matlabrc at 224
>> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------
Mon Aug 25 15:31:50 JST 2008
mcparams2exterg: finished
------- ************************** -----------
------- Motion Correcting Run 005 -----------
------- ************************** -----------
sess = mgh-101.1
Mon Aug 25 15:31:51 JST 2008
mc-afni2 --i 005/f.nii --t 003/f.nii --frame 0 --o 005/fmc.nii --mcdat
005/fmc.mcdat
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
mri_info --nframes --o /tmp/mriinfo.1882 003/f.nii
log file is 005/fmc.nii.mclog
mcdat file is 005/fmc.mcdat
tmp dir is 005/tmp.mc-afni2.1882
[EMAIL PROTECTED] --------------------------------
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
mri_convert 003/f.nii 005/tmp.mc-afni2.1882/tempvol.nii.gz --nskip 0 --ndrop 84
-odt float
mri_convert 003/f.nii 005/tmp.mc-afni2.1882/tempvol.nii.gz --nskip 0 --ndrop 84
-odt float
nskip = 0
ndrop = 84
$Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $
reading from 003/f.nii...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.9973, -0.0712038, 0.0179835)
j_ras = (0.0625429, -0.951817, -0.300222)
k_ras = (0.038494, -0.298286, 0.9537)
changing data type from 4 to 3 (noscale = 0)...
Dropping last 84 frames
writing to 005/tmp.mc-afni2.1882/tempvol.nii.gz...
[EMAIL PROTECTED] --------------------------------
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
mri_convert 005/f.nii 005/tmp.mc-afni2.1882/invol.nii.gz -odt float
mri_convert 005/f.nii 005/tmp.mc-afni2.1882/invol.nii.gz -odt float
$Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $
reading from 005/f.nii...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.9973, -0.0712038, 0.0179835)
j_ras = (0.0625429, -0.951817, -0.300222)
k_ras = (0.038494, -0.298286, 0.9537)
changing data type from 4 to 3 (noscale = 0)...
writing to 005/tmp.mc-afni2.1882/invol.nii.gz...
[EMAIL PROTECTED] --------------------------------
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
3dvolreg -verbose -dfile 005/fmc.mcdat -base
005/tmp.mc-afni2.1882/tempvol.nii.gz -prefix
005/tmp.mc-afni2.1882/outvol.nii.gz 005/tmp.mc-afni2.1882/invol.nii.gz
++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Aug 21 2008) [32-bit]
++ Authored by: RW Cox
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as 005/tmp.mc-afni2.1882/tempvol.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:005/tmp.mc-afni2.1882/tempvol.nii.gz is 17.858484 degrees
from plumb.
++ Reading in base dataset 005/tmp.mc-afni2.1882/tempvol.nii.gz
++ Oblique dataset:005/tmp.mc-afni2.1882/invol.nii.gz is 17.858484 degrees from
plumb.
++ Reading input dataset 005/tmp.mc-afni2.1882/invol.nii.gz
++ Edging: x=3 y=3 z=2
++ Creating mask for -maxdisp
+ Automask has 35297 voxels
+ 5257 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 85 sub-bricks:
0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..
++ CPU time for realignment=4.25 s [=0.05 s/sub-brick]
++ Min : roll=-0.057 pitch=+0.034 yaw=-0.063 dS=+0.044 dL=-0.184 dP=-0.108
++ Mean: roll=-0.005 pitch=+0.104 yaw=-0.002 dS=+0.204 dL=-0.030 dP=-0.035
++ Max : roll=+0.021 pitch=+0.335 yaw=+0.038 dS=+0.704 dL=+0.080 dP=+0.005
++ Max displacements (mm) for each sub-brick:
0.19 0.24 0.21 0.20 0.19 0.17 0.17 0.16 0.17 0.19 0.16 0.17 0.20 0.20 0.21
0.20 0.18 0.18 0.16 0.15 0.15 0.15 0.13 0.14 0.15 0.18 0.16 0.14 0.15 0.15 0.17
0.17 0.16 0.16 0.17 0.19 0.19 0.20 0.18 0.18 0.17 0.17 0.16 0.13 0.11 0.14 0.19
0.22 0.23 0.27 0.19 0.56 0.42 0.40 0.58 0.61 0.61 0.60 0.56 0.53 0.56 0.72 1.09
1.28 1.12 0.53 0.50 0.54 0.63 0.64 0.68 0.76 0.72 0.73 0.74 0.74 0.74 0.70 0.70
0.68 0.67 0.78 0.87 0.71 0.88
++ Max displacement in automask = 1.28 (mm) at sub-brick 63
++ Wrote dataset to disk in 005/tmp.mc-afni2.1882/outvol.nii.gz
[EMAIL PROTECTED] --------------------------------
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
mri_convert 005/tmp.mc-afni2.1882/outvol.nii.gz 005/fmc.nii --in_like 003/f.nii
mri_convert 005/tmp.mc-afni2.1882/outvol.nii.gz 005/fmc.nii --in_like 003/f.nii
reading info from 003/f.nii...
$Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $
reading from 005/tmp.mc-afni2.1882/outvol.nii.gz...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.9973, -0.0712038, 0.0179835)
j_ras = (0.0625429, -0.951817, -0.300222)
k_ras = (0.038494, -0.298286, 0.9537)
writing to 005/fmc.nii...
... cleaning up ....
Mon Aug 25 15:32:41 JST 2008
mc-afni2 done
INFO: Making external regressor from mc params
mcparams2extreg -mcfile 005/fmc.mcdat -northog 6 -extreg 005/mcextreg
Logfile is 005/mcparams2extreg.log
----------- Matlab file --------------
mcfile = '005/fmc.mcdat';
extreg = '005/mcextreg';
nkeep = [];
northog = [6];
pctorthog = [];
monly = 0;
mc = textread(mcfile);
mc = mc(:,2:7);
ntrs = size(mc,1);
if(ntrs < 6)
fprintf('ERROR: ntrs = %d < 6\n',ntrs);
if(~monly)
fprintf('Quiting matlab\n');
quit;
fprintf('should not be here\n');
end
end
if(~isempty(nkeep))
x = mc(:,1:nkeep);
elseif(~isempty(northog))
[u s v] = svd(mc);
ds = diag(s);
pct = 100*cumsum(ds)/sum(ds);
x = u(:,1:northog);
nkeep = northog;
fprintf('INFO: northog = %d, pct = %g\n',northog,pct(nkeep));
else
[u s v] = svd(mc);
ds = diag(s);
pct = 100*cumsum(ds)/sum(ds);
nkeep = min(find(pct > pctorthog));
x = u(:,1:nkeep);
fprintf('INFO: pctorthog = %g, nkeep = %d\n',pctorthog,nkeep);
end
x2 = zeros(1,1,nkeep,ntrs);
x2(1,1,:,:) = x'; %'
%fmri_svbvolume(x2,extreg);
mri.vol = permute(x2,[1 3 2 4]);
mri.tr = 0;
mri.flip_angle = 0;
mri.te = 0;
mri.ti = 0;
mri.vox2ras0 = eye(4);
mri.xsize = 1;
mri.ysize = 1;
mri.zsize = 1;
mri.volres = [1 1 1];
mri.volsize = [size(mri.vol,1) size(mri.vol,2) size(mri.vol,3)];
fname = sprintf('%s.bhdr',extreg);
MRIwrite(mri,fname);
quit;
-----------------------------------
------------------------------------------
------- matlab output --------------------
Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.
Warning:
MATLAB is starting without a display, using internal event queue.
You will not be able to display graphics on the screen.
< M A T L A B >
Copyright 1984-2005 The MathWorks, Inc.
Version 7.1.0.183 (R14) Service Pack 3
August 02, 2005
Warning: Duplicate directory name: /Users/eiji/matlab.
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Warning: Executing startup failed in matlabrc.
This indicates a potentially serious problem in your MATLAB setup,
which should be resolved as soon as possible. Error detected was:
MATLAB:UndefinedFunction
Undefined command/function 'setenv'.
> In matlabrc at 224
>> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------
Mon Aug 25 15:32:49 JST 2008
mcparams2exterg: finished
------- ************************** -----------
------- Motion Correcting Run 007 -----------
------- ************************** -----------
sess = mgh-101.1
Mon Aug 25 15:32:49 JST 2008
mc-afni2 --i 007/f.nii --t 003/f.nii --frame 0 --o 007/fmc.nii --mcdat
007/fmc.mcdat
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
mri_info --nframes --o /tmp/mriinfo.2252 003/f.nii
log file is 007/fmc.nii.mclog
mcdat file is 007/fmc.mcdat
tmp dir is 007/tmp.mc-afni2.2252
[EMAIL PROTECTED] --------------------------------
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
mri_convert 003/f.nii 007/tmp.mc-afni2.2252/tempvol.nii.gz --nskip 0 --ndrop 84
-odt float
mri_convert 003/f.nii 007/tmp.mc-afni2.2252/tempvol.nii.gz --nskip 0 --ndrop 84
-odt float
nskip = 0
ndrop = 84
$Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $
reading from 003/f.nii...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.9973, -0.0712038, 0.0179835)
j_ras = (0.0625429, -0.951817, -0.300222)
k_ras = (0.038494, -0.298286, 0.9537)
changing data type from 4 to 3 (noscale = 0)...
Dropping last 84 frames
writing to 007/tmp.mc-afni2.2252/tempvol.nii.gz...
[EMAIL PROTECTED] --------------------------------
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
mri_convert 007/f.nii 007/tmp.mc-afni2.2252/invol.nii.gz -odt float
mri_convert 007/f.nii 007/tmp.mc-afni2.2252/invol.nii.gz -odt float
$Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $
reading from 007/f.nii...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.9973, -0.0712038, 0.0179835)
j_ras = (0.0625429, -0.951817, -0.300222)
k_ras = (0.038494, -0.298286, 0.9537)
changing data type from 4 to 3 (noscale = 0)...
writing to 007/tmp.mc-afni2.2252/invol.nii.gz...
[EMAIL PROTECTED] --------------------------------
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
3dvolreg -verbose -dfile 007/fmc.mcdat -base
007/tmp.mc-afni2.2252/tempvol.nii.gz -prefix
007/tmp.mc-afni2.2252/outvol.nii.gz 007/tmp.mc-afni2.2252/invol.nii.gz
++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Aug 21 2008) [32-bit]
++ Authored by: RW Cox
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as 007/tmp.mc-afni2.2252/tempvol.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:007/tmp.mc-afni2.2252/tempvol.nii.gz is 17.858484 degrees
from plumb.
++ Reading in base dataset 007/tmp.mc-afni2.2252/tempvol.nii.gz
++ Oblique dataset:007/tmp.mc-afni2.2252/invol.nii.gz is 17.858484 degrees from
plumb.
++ Reading input dataset 007/tmp.mc-afni2.2252/invol.nii.gz
++ Edging: x=3 y=3 z=2
++ Creating mask for -maxdisp
+ Automask has 35215 voxels
+ 5278 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 85 sub-bricks:
0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..
++ CPU time for realignment=5.61 s [=0.066 s/sub-brick]
++ Min : roll=-0.008 pitch=+0.175 yaw=-0.046 dS=+0.361 dL=-0.177 dP=-0.127
++ Mean: roll=+0.023 pitch=+0.243 yaw=-0.030 dS=+0.497 dL=-0.110 dP=-0.087
++ Max : roll=+0.062 pitch=+0.418 yaw=-0.002 dS=+0.567 dL=-0.032 dP=-0.055
++ Max displacements (mm) for each sub-brick:
0.80 0.73 0.82 0.78 0.82 0.83 0.90 0.94 0.88 0.93 0.99 1.00 0.94 1.15 1.01
0.91 0.98 1.00 1.02 0.99 0.97 0.97 0.97 0.95 0.97 0.96 0.92 0.96 0.95 0.95 0.96
0.99 0.99 0.97 0.95 0.94 0.96 0.94 0.93 0.93 0.94 0.94 0.93 0.92 0.95 0.95 0.91
0.91 0.92 0.94 0.96 1.06 0.95 0.96 0.95 0.94 0.94 0.93 0.93 0.92 0.84 0.86 0.88
0.90 0.89 0.86 0.86 0.92 0.89 0.88 0.78 0.67 0.77 0.80 0.83 0.85 0.84 0.83 0.80
0.78 0.78 0.82 0.81 0.78 0.96
++ Max displacement in automask = 1.15 (mm) at sub-brick 13
++ Wrote dataset to disk in 007/tmp.mc-afni2.2252/outvol.nii.gz
[EMAIL PROTECTED] --------------------------------
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
mri_convert 007/tmp.mc-afni2.2252/outvol.nii.gz 007/fmc.nii --in_like 003/f.nii
mri_convert 007/tmp.mc-afni2.2252/outvol.nii.gz 007/fmc.nii --in_like 003/f.nii
reading info from 003/f.nii...
$Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $
reading from 007/tmp.mc-afni2.2252/outvol.nii.gz...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.9973, -0.0712038, 0.0179835)
j_ras = (0.0625429, -0.951817, -0.300222)
k_ras = (0.038494, -0.298286, 0.9537)
writing to 007/fmc.nii...
... cleaning up ....
Mon Aug 25 15:33:41 JST 2008
mc-afni2 done
INFO: Making external regressor from mc params
mcparams2extreg -mcfile 007/fmc.mcdat -northog 6 -extreg 007/mcextreg
Logfile is 007/mcparams2extreg.log
----------- Matlab file --------------
mcfile = '007/fmc.mcdat';
extreg = '007/mcextreg';
nkeep = [];
northog = [6];
pctorthog = [];
monly = 0;
mc = textread(mcfile);
mc = mc(:,2:7);
ntrs = size(mc,1);
if(ntrs < 6)
fprintf('ERROR: ntrs = %d < 6\n',ntrs);
if(~monly)
fprintf('Quiting matlab\n');
quit;
fprintf('should not be here\n');
end
end
if(~isempty(nkeep))
x = mc(:,1:nkeep);
elseif(~isempty(northog))
[u s v] = svd(mc);
ds = diag(s);
pct = 100*cumsum(ds)/sum(ds);
x = u(:,1:northog);
nkeep = northog;
fprintf('INFO: northog = %d, pct = %g\n',northog,pct(nkeep));
else
[u s v] = svd(mc);
ds = diag(s);
pct = 100*cumsum(ds)/sum(ds);
nkeep = min(find(pct > pctorthog));
x = u(:,1:nkeep);
fprintf('INFO: pctorthog = %g, nkeep = %d\n',pctorthog,nkeep);
end
x2 = zeros(1,1,nkeep,ntrs);
x2(1,1,:,:) = x'; %'
%fmri_svbvolume(x2,extreg);
mri.vol = permute(x2,[1 3 2 4]);
mri.tr = 0;
mri.flip_angle = 0;
mri.te = 0;
mri.ti = 0;
mri.vox2ras0 = eye(4);
mri.xsize = 1;
mri.ysize = 1;
mri.zsize = 1;
mri.volres = [1 1 1];
mri.volsize = [size(mri.vol,1) size(mri.vol,2) size(mri.vol,3)];
fname = sprintf('%s.bhdr',extreg);
MRIwrite(mri,fname);
quit;
-----------------------------------
------------------------------------------
------- matlab output --------------------
Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.
Warning:
MATLAB is starting without a display, using internal event queue.
You will not be able to display graphics on the screen.
< M A T L A B >
Copyright 1984-2005 The MathWorks, Inc.
Version 7.1.0.183 (R14) Service Pack 3
August 02, 2005
Warning: Duplicate directory name: /Users/eiji/matlab.
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Warning: Executing startup failed in matlabrc.
This indicates a potentially serious problem in your MATLAB setup,
which should be resolved as soon as possible. Error detected was:
MATLAB:UndefinedFunction
Undefined command/function 'setenv'.
> In matlabrc at 224
>> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------
Mon Aug 25 15:33:49 JST 2008
mcparams2exterg: finished
------- ************************** -----------
------- Motion Correcting Run 010 -----------
------- ************************** -----------
sess = mgh-101.1
Mon Aug 25 15:33:49 JST 2008
mc-afni2 --i 010/f.nii --t 003/f.nii --frame 0 --o 010/fmc.nii --mcdat
010/fmc.mcdat
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
mri_info --nframes --o /tmp/mriinfo.2609 003/f.nii
log file is 010/fmc.nii.mclog
mcdat file is 010/fmc.mcdat
tmp dir is 010/tmp.mc-afni2.2609
[EMAIL PROTECTED] --------------------------------
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
mri_convert 003/f.nii 010/tmp.mc-afni2.2609/tempvol.nii.gz --nskip 0 --ndrop 84
-odt float
mri_convert 003/f.nii 010/tmp.mc-afni2.2609/tempvol.nii.gz --nskip 0 --ndrop 84
-odt float
nskip = 0
ndrop = 84
$Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $
reading from 003/f.nii...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.9973, -0.0712038, 0.0179835)
j_ras = (0.0625429, -0.951817, -0.300222)
k_ras = (0.038494, -0.298286, 0.9537)
changing data type from 4 to 3 (noscale = 0)...
Dropping last 84 frames
writing to 010/tmp.mc-afni2.2609/tempvol.nii.gz...
[EMAIL PROTECTED] --------------------------------
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
mri_convert 010/f.nii 010/tmp.mc-afni2.2609/invol.nii.gz -odt float
mri_convert 010/f.nii 010/tmp.mc-afni2.2609/invol.nii.gz -odt float
$Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $
reading from 010/f.nii...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.9973, -0.0712038, 0.0179835)
j_ras = (0.0625429, -0.951817, -0.300222)
k_ras = (0.038494, -0.298286, 0.9537)
changing data type from 4 to 3 (noscale = 0)...
writing to 010/tmp.mc-afni2.2609/invol.nii.gz...
[EMAIL PROTECTED] --------------------------------
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
3dvolreg -verbose -dfile 010/fmc.mcdat -base
010/tmp.mc-afni2.2609/tempvol.nii.gz -prefix
010/tmp.mc-afni2.2609/outvol.nii.gz 010/tmp.mc-afni2.2609/invol.nii.gz
++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Aug 21 2008) [32-bit]
++ Authored by: RW Cox
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as 010/tmp.mc-afni2.2609/tempvol.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:010/tmp.mc-afni2.2609/tempvol.nii.gz is 17.858484 degrees
from plumb.
++ Reading in base dataset 010/tmp.mc-afni2.2609/tempvol.nii.gz
++ Oblique dataset:010/tmp.mc-afni2.2609/invol.nii.gz is 17.858484 degrees from
plumb.
++ Reading input dataset 010/tmp.mc-afni2.2609/invol.nii.gz
++ Edging: x=3 y=3 z=2
++ Creating mask for -maxdisp
+ Automask has 35100 voxels
+ 5266 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 85 sub-bricks:
0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..
++ CPU time for realignment=5.42 s [=0.0638 s/sub-brick]
++ Min : roll=+0.035 pitch=+0.179 yaw=-0.066 dS=+0.373 dL=-0.229 dP=-0.191
++ Mean: roll=+0.059 pitch=+0.268 yaw=-0.030 dS=+0.519 dL=-0.181 dP=-0.102
++ Max : roll=+0.087 pitch=+0.526 yaw=+0.016 dS=+0.685 dL=-0.104 dP=-0.067
++ Max displacements (mm) for each sub-brick:
0.85 0.86 0.94 1.03 1.25 1.18 1.17 1.17 1.14 1.02 0.96 1.00 1.10 1.06 1.02
1.02 0.99 0.99 0.99 1.00 0.75 0.82 0.94 0.93 0.97 1.01 0.99 1.03 0.99 1.30 1.01
1.00 1.02 0.93 0.95 0.97 0.90 0.91 0.93 0.90 0.92 0.95 0.95 0.95 1.05 1.06 1.07
1.07 1.07 1.07 0.99 0.94 0.89 0.77 0.86 0.87 0.89 0.91 0.98 1.00 0.98 0.95 0.94
0.95 0.92 0.89 0.91 0.95 0.96 0.99 0.99 0.99 0.96 0.94 1.17 1.04 0.98 0.92 0.89
0.91 0.94 1.30 1.38 1.26 1.18
++ Max displacement in automask = 1.38 (mm) at sub-brick 82
++ Wrote dataset to disk in 010/tmp.mc-afni2.2609/outvol.nii.gz
[EMAIL PROTECTED] --------------------------------
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
mri_convert 010/tmp.mc-afni2.2609/outvol.nii.gz 010/fmc.nii --in_like 003/f.nii
mri_convert 010/tmp.mc-afni2.2609/outvol.nii.gz 010/fmc.nii --in_like 003/f.nii
reading info from 003/f.nii...
$Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $
reading from 010/tmp.mc-afni2.2609/outvol.nii.gz...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.9973, -0.0712038, 0.0179835)
j_ras = (0.0625429, -0.951817, -0.300222)
k_ras = (0.038494, -0.298286, 0.9537)
writing to 010/fmc.nii...
... cleaning up ....
Mon Aug 25 15:34:41 JST 2008
mc-afni2 done
INFO: Making external regressor from mc params
mcparams2extreg -mcfile 010/fmc.mcdat -northog 6 -extreg 010/mcextreg
Logfile is 010/mcparams2extreg.log
----------- Matlab file --------------
mcfile = '010/fmc.mcdat';
extreg = '010/mcextreg';
nkeep = [];
northog = [6];
pctorthog = [];
monly = 0;
mc = textread(mcfile);
mc = mc(:,2:7);
ntrs = size(mc,1);
if(ntrs < 6)
fprintf('ERROR: ntrs = %d < 6\n',ntrs);
if(~monly)
fprintf('Quiting matlab\n');
quit;
fprintf('should not be here\n');
end
end
if(~isempty(nkeep))
x = mc(:,1:nkeep);
elseif(~isempty(northog))
[u s v] = svd(mc);
ds = diag(s);
pct = 100*cumsum(ds)/sum(ds);
x = u(:,1:northog);
nkeep = northog;
fprintf('INFO: northog = %d, pct = %g\n',northog,pct(nkeep));
else
[u s v] = svd(mc);
ds = diag(s);
pct = 100*cumsum(ds)/sum(ds);
nkeep = min(find(pct > pctorthog));
x = u(:,1:nkeep);
fprintf('INFO: pctorthog = %g, nkeep = %d\n',pctorthog,nkeep);
end
x2 = zeros(1,1,nkeep,ntrs);
x2(1,1,:,:) = x'; %'
%fmri_svbvolume(x2,extreg);
mri.vol = permute(x2,[1 3 2 4]);
mri.tr = 0;
mri.flip_angle = 0;
mri.te = 0;
mri.ti = 0;
mri.vox2ras0 = eye(4);
mri.xsize = 1;
mri.ysize = 1;
mri.zsize = 1;
mri.volres = [1 1 1];
mri.volsize = [size(mri.vol,1) size(mri.vol,2) size(mri.vol,3)];
fname = sprintf('%s.bhdr',extreg);
MRIwrite(mri,fname);
quit;
-----------------------------------
------------------------------------------
------- matlab output --------------------
Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.
Warning:
MATLAB is starting without a display, using internal event queue.
You will not be able to display graphics on the screen.
< M A T L A B >
Copyright 1984-2005 The MathWorks, Inc.
Version 7.1.0.183 (R14) Service Pack 3
August 02, 2005
Warning: Duplicate directory name: /Users/eiji/matlab.
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Warning: Executing startup failed in matlabrc.
This indicates a potentially serious problem in your MATLAB setup,
which should be resolved as soon as possible. Error detected was:
MATLAB:UndefinedFunction
Undefined command/function 'setenv'.
> In matlabrc at 224
>> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------
Mon Aug 25 15:34:49 JST 2008
mcparams2exterg: finished
Mon Aug 25 15:34:49 JST 2008
mc-sess completed SUCCESSFULLY
mgh-101.1 Smooth ------------------------
Mon Aug 25 15:34:49 JST 2008
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study
spatialsmooth-sess -i fmc -o fmcsm5 -fwhm 5 -fsd bold -s mgh-101.1 -d
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study
-update -noinorm
----------------------------------------
------------------------------------------------
------------------------------------------------
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1
Mon Aug 25 15:34:50 JST 2008
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study
RunList 003 005 007 010
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
ls: 003/fmcsm5.nii: No such file or directory
-rw-r--r-- 1 eiji wheel 48742752 Aug 25 15:31 003/fmc.nii
Update not needed
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
ls: 005/fmcsm5.nii: No such file or directory
-rw-r--r-- 1 eiji wheel 48742752 Aug 25 15:32 005/fmc.nii
Update not needed
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
ls: 007/fmcsm5.nii: No such file or directory
-rw-r--r-- 1 eiji wheel 48742752 Aug 25 15:33 007/fmc.nii
Update not needed
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
ls: 010/fmcsm5.nii: No such file or directory
-rw-r--r-- 1 eiji wheel 48742752 Aug 25 15:34 010/fmc.nii
Update not needed
Started at Mon Aug 25 15:34:50 JST 2008
Ended at Mon Aug 25 15:34:53 JST 2008
spatiallysmooth-sess Done
mgh-101.1 Inorm ------------------------
Mon Aug 25 15:34:53 JST 2008
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study
mkbrainmask-sess -maskstem brain -fsd bold -s mgh-101.1 -d
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study
-update
----------------------------------------
------------------------------------------------
------------------------------------------------
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1
Mon Aug 25 15:34:54 JST 2008
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/fsfast-tutorial/my-study/mgh-101.1/bold
ls: masks/brain.nii: No such file or directory
-rw-r--r-- 1 eiji wheel 24371552 Aug 22 17:33 003/f.nii
Update not needed
Mon Aug 25 15:34:56 JST 2008
mkbrainmask-sess done
----------------------------------------
Started at Mon Aug 25 15:30:40 JST 2008
Ended at Mon Aug 25 15:34:56 JST 2008
preproc-sess done
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
