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.eduwrote:
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.eduwrote:
Can you send me the matlab file? And what version of matlab are you running? On the mac, you'll probably have to copy it to your home directly, edit it, then copy it back. When you copy it back, you'll have to sudo to get administrator privileges.
doug
On 4/25/11 4:26 PM, Maryam Vaziri Pashkam wrote:
There is an error:
??? Error: Unexpected MATLAB operator when I run matlab -r matlabfile.m I wanted to change the mcparams2extreg to see if it works but I don't know how to change it and where it is located.
Maryam
On Mon, Apr 25, 2011 at 3:22 PM, Douglas Greve <greve@nmr.mgh.harvard.edu
wrote:
Yea, I vaguely remember this problem with 4.5 and the macs. Try running this from a terminal (not from matlab):
matlab -r matlabfile.m
where matlabfile.m is the file created with -monly. If this works you can change the call to matlab from mcparams2extreg from
cat $MLF | $MATLAB -display iconic | tee -a $LF
to
$MATLAB -r $MLF -display iconic | tee -a $LF
doug
On 4/25/11 2:49 PM, Maryam Vaziri Pashkam wrote:
Hi Dough,
The generated matlab programs works from within matlab and generates mcextreg.bhdr and mcextreg_000.bfloat and mcextreg_000.hdr.
It seems that there is a problem calling matlab from terminal? any idea how I can fix this? I have two versions on Matlab on my computer. Could this be a source of the problem? I checked the program in both matlabs and it works when run from inside Matlab.
Maryam
On Mon, Apr 25, 2011 at 4:32 AM, Douglas Greve < greve@nmr.mgh.harvard.edu> wrote:
Try running mcparams2extreg with the -monly option to create a matlab file. Then run that matlab file from inside matlab. If that fails in the same way, send me the matlab file.
doug
On 4/25/11 4:02 AM, Maryam Vaziri Pashkam wrote:
Hi Dough,
I have attached the log file. It does not give any extra information. I ran the command you told me and gave me the exact same errors. It looks like there is a problem with that command and reading of the fmc.mcdat file. I have also attached the fmc.mcdat file from run 6. Any other idea?
Thanks, Maryam
On Mon, Apr 25, 2011 at 3:44 AM, < freesurfer-request@nmr.mgh.harvard.edu> wrote:
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Today's Topics:
- Fwd: error with motion correction (Maryam Vaziri Pashkam)
- 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, 2009To 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
freesurfer@nmr.mgh.harvard.edu
-
Maryam Vaziri Pashkam