I'm not sure where to proceed next. I can't create the error on my mac, so
it must be something about your version of matlab/macos. Let's go back to
trying  the matlab -r command. Is this what you did:

cd session/bold
mcparams2extreg -extreg junk.txt -mcfile RRR/fmc.mcdat -nkeep 6 -monly
mcp2x.m
matlab -r mcp2x

It should not have generated the same error as when using mcp2x.m.

Can you also try
cat mcp2x.m | matlab

doug

> 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:
>>>>>
>>>>>> Send Freesurfer mailing list submissions to
>>>>>>        freesurfer@nmr.mgh.harvard.edu
>>>>>>
>>>>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>>>>        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> or, via email, send a message with subject or body 'help' to
>>>>>>        freesurfer-request@nmr.mgh.harvard.edu
>>>>>>
>>>>>> You can reach the person managing the list at
>>>>>>        freesurfer-owner@nmr.mgh.harvard.edu
>>>>>>
>>>>>> When replying, please edit your Subject line so it is more specific
>>>>>> than "Re: Contents of Freesurfer digest..."
>>>>>>
>>>>>>
>>>>>> 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 <005%20006%20007%20008> 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
>>>>>> >
>>>>>> >
>>>>>> >

>>>>>> > _______________________________________________
>>>>>> > Freesurfer mailing list
>>>>>> > Freesurfer@nmr.mgh.harvard.edu

>>>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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>>>>>> ------------------------------
>>>>>>
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu

>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>

>>>>>> End of Freesurfer Digest, Vol 86, Issue 77
>>>>>> ******************************************
>>>>>>
>>>>>>
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>>>>>> addressed. If you believe this e-mail was sent to you in error and
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>>>>>> contains patient information, please contact the Partners Compliance
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>>>>>
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>>
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