I think the reason you get that type of error is because Matlab thinks you are trying to reference a variable called 'm' which is a member of a struct called 'matlabfile'. Since the 'm' variable doesn't exist, it is "unexpected".
On Tue, 26 Apr 2011, Douglas Greve wrote: > Oh, that's right, forgot that you don't give it the .m. The problem with > using this method was that it would not automatically quit when it got > to the end of the script (or if there was an error in the script, it > would just hang there). Any ideas how to overcome that? > > thanks > doug > > On 4/26/11 11:27 AM, Louis Nicholas Vinke wrote: >> Try running the command without the '.m'. >> -Louis >> >> On Mon, 25 Apr 2011, 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<gr...@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<gr...@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-requ...@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-requ...@nmr.mgh.harvard.edu >>>>>> >>>>>> You can reach the person managing the list at >>>>>> freesurfer-ow...@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<mvazir...@gmail.com> >>>>>> Subject: [Freesurfer] Fwd: error with motion correction >>>>>> To: freesurfer@nmr.mgh.harvard.edu >>>>>> Message-ID:<banlktikkajvqp5bxvd5e2mowqvwbrev...@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<gr...@nmr.mgh.harvard.edu> >>>>>> Subject: Re: [Freesurfer] Fwd: error with motion correction >>>>>> To: freesurfer@nmr.mgh.harvard.edu >>>>>> Message-ID:<4db5263f.2060...@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 >>>>>> -------------- next part -------------- >>>>>> An HTML attachment was scrubbed... >>>>>> URL: >>>>>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110425/d7a55eb3/attachment.html >>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>>> ****************************************** >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to whom it >>>>>> is >>>>>> addressed. 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