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. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>>> in error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>>> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
