HI Doug,

Did you get the file I sent you?

Any new idea about how I can fix the problem?

Maryam

On Tue, Apr 26, 2011 at 5:25 AM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

The file will be found in $FREESURFER_HOME/fsfast/bin/mcparams2extreg, but until we figure out how to run matlab in a way that does not crash, it will not do any good to edit this file. Actually, can you send me your version of mcparams2extreg? I ran your matlab file on my mac by catting it to matlab, but it failed with I tried to run it with -r (don't know why).

doug

On 4/25/11 4:41 PM, Maryam Vaziri Pashkam wrote:

Here is the m file.

I have two versions of Matlab: R2008a, R2009b. The one that freesurfer runs when calling matlab codes in 2009b.

Sorry I am not sure what I should copy to my home directory and edit. I thought the line you asked me to change was in the mcparams2extreg file which I don't know where it is. Could you explain a bit more?

Maryam

On Mon, Apr 25, 2011 at 4:34 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

Can you send me the matlab file? And what version of matlab are you running? On the mac, you'll probably have to copy it to your home directly, edit it, then copy it back. When you copy it back, you'll have to sudo to get administrator privileges.

doug

On 4/25/11 4:26 PM, Maryam Vaziri Pashkam wrote:

There is an error:

??? Error: Unexpected MATLAB operator when I run matlab -r matlabfile.m

I wanted to change the mcparams2extreg to see if it works but I don't know how to change it and where it is located.

Maryam

On Mon, Apr 25, 2011 at 3:22 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

Yea, I vaguely remember this problem with 4.5 and the macs. Try running this from a terminal (not from matlab):

matlab -r matlabfile.m

where matlabfile.m is the file created with -monly. If this works you can change the call to matlab from mcparams2extreg from

cat $MLF | $MATLAB -display iconic | tee -a $LF

to

$MATLAB -r $MLF -display iconic | tee -a $LF

doug

On 4/25/11 2:49 PM, Maryam Vaziri Pashkam wrote:

Hi Dough,

The generated matlab programs works from within matlab and generates mcextreg.bhdr and mcextreg_000.bfloat and mcextreg_000.hdr.

It seems that there is a problem calling matlab from terminal? any idea how I can fix this? I have two versions on Matlab on my computer. Could this be a source of the problem? I checked the program in both matlabs and it works when run from inside Matlab.

Maryam

On Mon, Apr 25, 2011 at 4:32 AM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

Try running mcparams2extreg with the -monly option to create a matlab file. Then run that matlab file from inside matlab. If that fails in the same way, send me the matlab file.

doug

On 4/25/11 4:02 AM, Maryam Vaziri Pashkam wrote:

Hi Dough,

I have attached the log file. It does not give any extra information. I ran the command you told me and gave me the exact same errors. It looks like there is a problem with that command and reading of the fmc.mcdat file. I have also attached the fmc.mcdat file from run 6.

Any other idea?

Thanks,

Maryam

On Mon, Apr 25, 2011 at 3:44 AM, <freesurfer-request@nmr.mgh.harvard.edu> wrote:

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Today's Topics:

1. Fwd: error with motion correction (Maryam Vaziri Pashkam)
2. Re: Fwd: error with motion correction (Douglas Greve)

----------------------------------------------------------------------

Message: 1
Date: Sun, 24 Apr 2011 21:01:43 -0400
From: Maryam Vaziri Pashkam <mvaziri.p@gmail.com>
Subject: [Freesurfer] Fwd: error with motion correction
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <BANLkTikkaJvqP5bxVD5e2moWQvwBrev9iA@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110424/7835b719/attachment-0001.html

------------------------------

Message: 2
Date: Mon, 25 Apr 2011 03:43:59 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Fwd: error with motion correction
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <4DB5263F.2060902@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"

Hi Maryam, I don't know what is going on. Does 006/mcparams2extreg.log
have anymore information? Can you run

cd 110419_xu_PDM1_02_PDM/bold
mcparams2extreg -mcfile 006/fmc.mcdat -northog 6 -extreg 006/mcextreg

doug

On 4/24/11 9:01 PM, Maryam Vaziri Pashkam wrote:
>
> 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 <http://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
> <http://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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> Freesurfer@nmr.mgh.harvard.edu
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