Thanks, Doug.
Any ideas why preproc-sess does not generate fmcsm5.nii and masks/
brain.nii?
Eiji
On 2008/08/26, at 0:12, Doug Greve wrote:
The two warnings are unimportant. The error about the "Undefined
command/function 'setenv'. " is probably a problem with your matlab/
startup.m file. Looks like you put a 'setenv' command in there.
doug
N. Eiji Nawa wrote:
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..3
7..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..7
2..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..3
7..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..7
2..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..3
7..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..7
2..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..3
7..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..7
2..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
-- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED]
Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us
help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/
fswiki/BugReporting
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
