Hi,
I've tried a few more things since posting my last message but have still not
been able to solve the problem with mc-sess where it hangs.
I got rid of the Matlab process manager error by using Matlab 6, but the motion
correction process still hangs after opening Matlab and printing
INFO: northog = 6, pct=100.
I also tried to use the bert dataset and had the same output and then it hanged.
The exact command I used was mc-sess -sf sessid -df sesspar
I use the PowerPC version of freesurferv4.0.1.
Any help would be appreciated. I attach the log file generated by mc-sess with
this email.
Leila
---------------------------------------------------------------------
FREESURFER_HOME: /Software/freesurfer
Build stamp: freesurfer-Darwin-tiger-stable-pub-v4.0.1
Kernel info: Darwin 8.10.0 Power Macintosh
---------------------------------------------------------------------
------------------------------
Message: 3
Date: Tue, 13 Nov 2007 22:08:45 -0500
From: Leila Reddy <[EMAIL PROTECTED]>
Subject: [Freesurfer] Error with mc-sess
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1
Hi,
I recently installed freesurfer, AFNI etc but am having problems with mc-sess.
The script runs and gets to the stage in each run where it calls up matlab,
enters the MRIwrite command but then gives the message below. It then hangs.
INFO: northog = 6, pct = 100
2007-11-13
18:44:51.464 MATLAB[6569] Process manager already initialized -- can't fully
enable headless mode.
I can kill the process (e.g.6569 in the example above) and it moves on to the
next run, but without saving anything for the current run.
Does anyone know what I can do to fix it?
Thanks,
Leila
------------------------------
------------------------------------------------------------------------
mc-sess
bert
$Id: mc-sess,v 1.16 2007/06/18 02:22:02 greve Exp $
/Users/lreddy/Desktop/Leila-Data/FSFAST_Tutorial/StudyDirectory/log/mc-bert-bold.log
Darwin wagner.klab.caltech.edu 8.10.0 Darwin Kernel Version 8.10.0: Wed May 23
16:50:59 PDT 2007; root:xnu-792.21.3~1/RELEASE_PPC Power Macintosh powerpc
Thu Nov 15 16:48:41 PST 2007
-sf sessid -df sesspar
/Users/lreddy/Desktop/Leila-Data/FSFAST_Tutorial/StudyDirectory
ProjectDir /Users/lreddy/Desktop/Leila-Data/FSFAST_Tutorial/StudyDirectory
-------------------------------------------
/Users/lreddy/Desktop/Leila-Data/FSFAST_Tutorial/SessionParent/bert
RunList: 007 008 009
------- ************************** -----------
------- Motion Correcting Run 007 -----------
------- ************************** -----------
sess = bert
Thu Nov 15 16:48:43 PST 2007
mc-afni2 --i 007/f.bhdr --t 007/f.bhdr --frame 0 --o 007/fmc.nii --mcdat
007/fmc.mcdat
/Users/lreddy/Desktop/Leila-Data/FSFAST_Tutorial/SessionParent/bert/bold
mri_info --nframes --o /tmp/mriinfo.13039 007/f.bhdr
log file is 007/fmc.nii.mclog
mcdat file is 007/fmc.mcdat
tmp dir is 007/tmp.mc-afni2.13039
[EMAIL PROTECTED] --------------------------------
/Users/lreddy/Desktop/Leila-Data/FSFAST_Tutorial/SessionParent/bert/bold
mri_convert 007/f.bhdr 007/tmp.mc-afni2.13039/tempvol.nii.gz --nskip 0 --ndrop
179 -odt float
mri_convert 007/f.bhdr 007/tmp.mc-afni2.13039/tempvol.nii.gz --nskip 0 --ndrop 179 -odt float
nskip = 0
ndrop = 179
$Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $
reading from 007/f.bhdr...
INFO: bvolumeRead: min = 0, max = 928
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -0.920505, -0.390731)
k_ras = (0, 0.390731, -0.920505)
changing data type from 4 to 3 (noscale = 0)...
Dropping last 179 frames
writing to 007/tmp.mc-afni2.13039/tempvol.nii.gz...
[EMAIL PROTECTED] --------------------------------
/Users/lreddy/Desktop/Leila-Data/FSFAST_Tutorial/SessionParent/bert/bold
mri_convert 007/f.bhdr 007/tmp.mc-afni2.13039/invol.nii.gz -odt float
mri_convert 007/f.bhdr 007/tmp.mc-afni2.13039/invol.nii.gz -odt float
$Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $
reading from 007/f.bhdr...
INFO: bvolumeRead: min = 0, max = 928
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -0.920505, -0.390731)
k_ras = (0, 0.390731, -0.920505)
changing data type from 4 to 3 (noscale = 0)...
writing to 007/tmp.mc-afni2.13039/invol.nii.gz...
[EMAIL PROTECTED] --------------------------------
/Users/lreddy/Desktop/Leila-Data/FSFAST_Tutorial/SessionParent/bert/bold
3dvolreg -verbose -dfile 007/fmc.mcdat -base
007/tmp.mc-afni2.13039/tempvol.nii.gz -prefix
007/tmp.mc-afni2.13039/outvol.nii.gz 007/tmp.mc-afni2.13039/invol.nii.gz
++ 3dvolreg: AFNI version=AFNI_2007_05_29_1644 (Nov 9 2007) [32-bit]
++ Authored by: RW Cox
qform not present, sform used.
sform was not exact, and the worst axis is
22.999998 degrees from plumb.
++ Reading in base dataset 007/tmp.mc-afni2.13039/tempvol.nii.gz
qform not present, sform used.
sform was not exact, and the worst axis is
22.999998 degrees from plumb.
++ Reading input dataset 007/tmp.mc-afni2.13039/invol.nii.gz
++ Edging: x=3 y=3 z=1
++ Creating mask for -maxdisp
+ Automask has 25853 voxels
+ 5127 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 180 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..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..
++ CPU time for realignment=5.72 s [=0.0318 s/sub-brick]
++ Min : roll=-0.294 pitch=-0.064 yaw=-0.500 dS=-0.516 dL=-0.337 dP=-0.558
++ Mean: roll=-0.068 pitch=+0.006 yaw=-0.317 dS=-0.134 dL=-0.067 dP=-0.171
++ Max : roll=+0.150 pitch=+0.094 yaw=-0.000 dS=+0.033 dL=+0.130 dP=+0.202
++ Max displacements (mm) for each sub-brick:
++ Max displacements (mm) for each sub-brick:
0.00 0.07 0.06 0.04 0.07 0.08 0.11 0.13 0.14 0.14 0.19 0.21 0.17 0.20 0.16 0.19
0.20 0.19 0.22 0.25 0.25 0.30 0.80 0.56 0.57 0.49 0.50 0.42 0.44 0.48 0.46 0.49
0.44 0.48 0.49 0.45 0.53 0.49 0.46 0.50 0.46 0.48 0.51 0.44 0.48 0.49 0.44 0.52
0.48 0.51 0.51 0.50 0.55 0.51 0.57 0.54 0.52 0.54 0.53 0.52 0.57 0.55 0.55 0.58
0.56 0.59 0.57 0.54 0.58 0.58 0.57 0.56 0.53 0.55 0.54 0.51 0.55 0.66 0.55 0.55
0.57 0.57 0.72 0.62 0.68 0.62 0.62 0.62 0.62 0.67 0.67 0.70 0.75 0.69 0.63 0.65
0.68 0.76 0.76 0.76 0.76 0.69 0.71 0.72 0.66 0.73 0.79 0.77 0.71 0.69 0.72 0.77
0.75 0.74 0.77 0.81 0.82 0.85 0.86 0.86 0.88 0.85 0.83 0.87 0.87 0.91 0.94 1.01
0.99 1.01 1.01 1.03 1.03 1.01 0.93 1.02 1.03 1.06 1.09 1.09 1.09 1.07 1.09 1.11
1.12 1.14 1.16 1.14 1.11 1.18 1.18 1.16 1.21 1.23 1.22 1.22 1.24 1.22 1.26 1.27
1.24 1.26 1.31 1.34 1.34 1.33 1.33 1.33 1.24 1.29 1.31 1.35 1.33 1.33 1.33 1.30
1.34 1.32 1.30 1.28
++ Max displacement in automask = 1.35 (mm) at sub-brick 171
++ Wrote dataset to disk in 007/tmp.mc-afni2.13039/outvol.nii.gz
** Warning: overwriting file 007/fmc.mcdat
[EMAIL PROTECTED] --------------------------------
/Users/lreddy/Desktop/Leila-Data/FSFAST_Tutorial/SessionParent/bert/bold
mri_convert 007/tmp.mc-afni2.13039/outvol.nii.gz 007/fmc.nii --in_like
007/f.bhdr
mri_convert 007/tmp.mc-afni2.13039/outvol.nii.gz 007/fmc.nii --in_like 007/f.bhdr
reading info from 007/f.bhdr...
$Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $
reading from 007/tmp.mc-afni2.13039/outvol.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -0.920505, -0.390731)
k_ras = (0, 0.390731, -0.920505)
writing to 007/fmc.nii...
... cleaning up ....
Thu Nov 15 16:49:48 PST 2007
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);
-----------------------------------
------------------------------------------
------- 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 1984-2006 The MathWorks, Inc.
Version 7.2.0.283 (R2006a)
January 27, 2006
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Warning: Duplicate directory name: /home/lreddy/matlab.
In path at 113
In startup at 380
In matlabrc at 216
INFO: northog = 6, pct = 100
------------------------------------------------------------------------
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