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 lreddy@MIT.EDU Subject: [Freesurfer] Error with mc-sess To: freesurfer@nmr.mgh.harvard.edu Message-ID: 20071113220845.pkqf8xeylhs8ggg8@webmail.mit.edu 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
------------------------------
Can you run any of the other matlab-based fsfast commands? I've never tried it on a power pc, so maybe the matlab version is slightly different (looks like it does not know when to quit).
You can try running it outside of mc-sess with:
cd /Users/lreddy/Desktop/Leila-Data/FSFAST_Tutorial/SessionParent/bert/bold mcparams2extreg -mcfile 007/fmc.mcdat -northog 6 -extreg 007/mcextreg
If this hangs, you can try:
mcparams2extreg -mcfile 007/fmc.mcdat -northog 6 -extreg 007/mcextreg -monly mcp.m
Then start matlab and run mcp.m to see if it finishes.
doug
lreddy@mit.edu wrote:
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 lreddy@MIT.EDU Subject: [Freesurfer] Error with mc-sess To: freesurfer@nmr.mgh.harvard.edu Message-ID: 20071113220845.pkqf8xeylhs8ggg8@webmail.mit.edu 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 #@# -------------------------------- /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... #@# -------------------------------- /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... #@# -------------------------------- /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 #@# -------------------------------- /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, 2006To 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 >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>------------------------------------------------------------------------ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>_______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>Freesurfer mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
lreddy＠MIT.EDU