Hi,
I am running into trouble with motion correction on my Mac and freesurfer
4.5.
Originally I ran preproc-sess and got an error from mc-sess in the part (i
think) that runs the mcextreg. I ran mc-sess and the same error happened (I
have copy pasted the log bellow).
It seems like the matlab program that runs mcparams2extreg cannot read the
fmc.mcdat file. when I did textread('fmc.mcdat') in matlab, I could open the
file and it looked perfectly fine to me with the correct number of TR's.
Any idea where the problem might be?
Maryam
preproc-sess -nosmooth -i f -sf sessid -df sessdir
--------------------------------------------------------------
preproc-sess logfile is log/preproc-sess.log
--------------------------------------------------------------
instem f
mc 1 f fmc
stc 0 fmc
sm 0
mask 1 brain
110419_xu_PDM1_02_PDM MC -----------------------------
Sun Apr 24 20:42:29 EDT 2011
/Users/maryam/mri-space/studies/PDM1/PDM1
mc-sess -fstem f -fmcstem fmc -s 110419_xu_PDM1_02_PDM -d
/Users/maryam/mri-space/studies/PDM1/unpackdata -fsd bold -new -update
-no-inorm
----------------------------------------
Logfile is
/Users/maryam/mri-space/studies/PDM1/PDM1/log/mc-110419_xu_PDM1_02_PDM-bold.log
-------------------------------------------
/Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM
RunList: 005 006 007 008 011 012 013 014
Targ Stem is 005/f
Update not needed
-rw-r--r-- 1 maryam staff 129203552 Apr 24 20:12 005/fmc.nii
-rw-r--r-- 1 maryam staff 64601952 Apr 24 19:12 005/f.nii
------- ************************** -----------
------- Motion Correcting Run 006 -----------
------- ************************** -----------
sess = 110419_xu_PDM1_02_PDM
Sun Apr 24 20:42:30 EDT 2011
mc-afni2 --i 006/f.nii --t 005/f.nii --frame 0 --o 006/fmc.nii --mcdat
006/fmc.mcdat
/Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold
mri_info --nframes --o /tmp/mriinfo.2758 005/f.nii
log file is 006/fmc.nii.mclog
mcdat file is 006/fmc.mcdat
tmp dir is 006/tmp.mc-afni2.2758
#@# --------------------------------
/Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold
mri_convert 005/f.nii 006/tmp.mc-afni2.2758/tempvol.nii.gz --nskip 0 --ndrop
205 -odt float
mri_convert 005/f.nii 006/tmp.mc-afni2.2758/tempvol.nii.gz --nskip 0 --ndrop
205 -odt float
nskip = 0
ndrop = 205
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from 005/f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0.000171665, -3.15037e-05)
j_ras = (0.000174532, -0.983572, -0.180519)
k_ras = (-2.07852e-18, -0.180519, 0.983572)
changing data type from 4 to 3 (noscale = 0)...
Dropping last 205 frames
writing to 006/tmp.mc-afni2.2758/tempvol.nii.gz...
#@# --------------------------------
/Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold
mri_convert 006/f.nii 006/tmp.mc-afni2.2758/invol.nii.gz -odt float
mri_convert 006/f.nii 006/tmp.mc-afni2.2758/invol.nii.gz -odt float
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from 006/f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0.000171665, -3.15037e-05)
j_ras = (0.000174532, -0.983572, -0.180519)
k_ras = (-2.07852e-18, -0.180519, 0.983572)
changing data type from 4 to 3 (noscale = 0)...
writing to 006/tmp.mc-afni2.2758/invol.nii.gz...
#@# --------------------------------
/Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold
3dvolreg -verbose -dfile 006/fmc.mcdat -base
006/tmp.mc-afni2.2758/tempvol.nii.gz -prefix
006/tmp.mc-afni2.2758/outvol.nii.gz 006/tmp.mc-afni2.2758/invol.nii.gz
++ 3dvolreg: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) [32-bit]
++ Authored by: RW Cox
*+ WARNING: If you are performing spatial transformations on an oblique
dset,
such as 006/tmp.mc-afni2.2758/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:006/tmp.mc-afni2.2758/tempvol.nii.gz is 10.399981 degrees
from plumb.
++ Reading in base dataset 006/tmp.mc-afni2.2758/tempvol.nii.gz
++ Oblique dataset:006/tmp.mc-afni2.2758/invol.nii.gz is 10.399981 degrees
from plumb.
++ Reading input dataset 006/tmp.mc-afni2.2758/invol.nii.gz
++ Edging: x=4 y=4 z=2
++ Creating mask for -maxdisp
+ Automask has 57667 voxels
+ 10333 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 206 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..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..
++ CPU time for realignment=16.6 s [=0.0808 s/sub-brick]
++ Min : roll=-0.008 pitch=-0.103 yaw=-0.096 dS=+0.255 dL=-0.019
dP=-0.151
++ Mean: roll=+0.031 pitch=-0.011 yaw=-0.045 dS=+0.619 dL=+0.037
dP=-0.055
++ Max : roll=+0.060 pitch=+0.112 yaw=-0.010 dS=+0.693 dL=+0.075
dP=+0.015
++ Max displacements (mm) for each sub-brick:
0.49 0.65 0.63 0.74 0.69 0.75 0.71 0.77 0.70 0.76 0.67 0.77 0.72 0.73 0.66
0.67 0.67 0.67 0.69 0.70 0.72 0.66 0.71 0.68 0.72 0.67 0.73 0.68 0.73 0.66
0.73 0.66 0.70 0.64 0.72 0.69 0.71 0.71 0.72 0.66 0.66 0.67 0.72 0.70 0.71
0.72 0.71 0.69 0.72 0.72 0.71 0.72 0.72 0.69 0.71 0.74 0.73 0.69 0.72 0.72
0.76 0.76 0.79 0.73 0.75 0.74 0.75 0.75 0.71 0.74 0.67 0.72 0.65 0.72 0.65
0.69 0.69 0.65 0.68 0.64 0.72 0.67 0.67 0.68 0.69 0.65 0.73 0.67 0.71 0.69
0.73 0.72 0.76 0.74 0.72 0.66 0.68 0.69 0.69 0.68 0.68 0.70 0.73 0.70 0.73
0.78 0.74 0.73 0.75 0.74 0.72 0.74 0.63 0.66 0.68 0.74 0.72 0.74 0.79 0.74
0.74 0.76 0.79 0.79 0.74 0.76 0.70 0.75 0.72 0.78 0.74 0.78 0.76 0.80 0.76
0.79 0.77 0.76 0.76 0.75 0.73 0.80 0.78 0.81 0.78 0.84 0.76 0.79 0.77 0.79
0.76 0.83 0.77 0.79 0.77 0.84 0.76 0.80 0.77 0.81 0.72 0.79 0.74 0.80 0.77
0.83 0.81 0.82 0.76 0.81 0.75 0.78 0.74 0.75 0.71 0.75 0.73 0.77 0.77 0.80
0.77 0.80 0.75 0.73 0.77 0.72 0.76 0.72 0.76 0.72 0.72 0.69 0.66 0.68 0.65
0.68 0.64 0.70 0.62 0.70 0.62 0.69 0.67 0.74 0.75 0.74
++ Max displacement in automask = 0.84 (mm) at sub-brick 145
++ Wrote dataset to disk in 006/tmp.mc-afni2.2758/outvol.nii.gz
#@# --------------------------------
/Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold
mri_convert 006/tmp.mc-afni2.2758/outvol.nii.gz 006/fmc.nii --in_like
005/f.nii
mri_convert 006/tmp.mc-afni2.2758/outvol.nii.gz 006/fmc.nii --in_like
005/f.nii
reading info from 005/f.nii...
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from 006/tmp.mc-afni2.2758/outvol.nii.gz...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0.000171665, -3.15037e-05)
j_ras = (0.000174532, -0.983572, -0.180519)
k_ras = (-2.07852e-18, -0.180519, 0.983572)
writing to 006/fmc.nii...
... cleaning up ....
Sun Apr 24 20:43:59 EDT 2011
mc-afni2 done
INFO: Making external regressor from mc params
mcparams2extreg -mcfile 006/fmc.mcdat -northog 6 -extreg 006/mcextreg
Logfile is 006/mcparams2extreg.log
----------- Matlab file --------------
mcfile = '006/fmc.mcdat';
extreg = '006/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'. You will not be able to display
graphics on the screen.
< M A T L A B (R) >
Copyright 1984-2009 The MathWorks, Inc.
Version 7.9.0.529 (R2009b) 64-bit (maci64)
August 12, 2009
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
>> >> >> >> >> >> >> >> ??? Error using ==> textread at 167
File not found.
>> ??? Undefined variable mc.
>> ??? Undefined function or variable 'mc'.
>> ??? Undefined function or variable 'ntrs'.
>> >> ??? Undefined function or variable 'mc'.
>> >> ??? Undefined function or variable 'ntrs'.
>> ??? Undefined function or variable 'x'.
>> >> >> ??? Undefined function or variable 'x2'.
>> >> >> >> >> >> >> >> >> >> ??? Reference to non-existent field 'vol'.
>> >> ??? Reference to non-existent field 'vol'.
Error in ==> MRIwrite at 70
bmri.voldim = [size(mri.vol,1) size(mri.vol,2) size(mri.vol,3)];
>> >> ------------------------------------------
ERROR: output not created
ERROR: mc-sess failed
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