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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