Freesurfer April 2011

freesurfer@nmr.mgh.harvard.edu

121 participants
166 discussions

Re: [Freesurfer] Freesurfer Digest, Vol 86, Issue 77
by Maryam Vaziri Pashkam 28 Apr '11

28 Apr '11

Hi, I tried "matlab -r mcp2x" and "matlab -r mcp2x.m" in both cased I get an error that "undefined function or variable mcp2x. I tried cat mcp2x.m | matlab, and the program runs and gives the exact same error as before when I ran mcparams2extreg from within terminal (see bellow). It looks like an error that occurs when you are in the wrong directory in matlab and you are calling a file from another directory which does not make sense as the fmc files are created in the correct path. Maryam >> >> >> >> >> >> >> >> ??? Error using ==> textread at 167 File not found. >> ??? Undefined variable mc. >> ??? Undefined function or variable 'mc'. >> ??? Undefined function or variable 'ntrs'. >> >> ??? Undefined 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)]; On Thu, Apr 28, 2011 at 8:52 AM, <greve(a)nmr.mgh.harvard.edu> wrote: > I'm not sure where to proceed next. I can't create the error on my mac, so > it must be something about your version of matlab/macos. Let's go back to > trying the matlab -r command. Is this what you did: > > cd session/bold > mcparams2extreg -extreg junk.txt -mcfile RRR/fmc.mcdat -nkeep 6 -monly > mcp2x.m > matlab -r mcp2x > > It should not have generated the same error as when using mcp2x.m. > > Can you also try > cat mcp2x.m | matlab > > doug > > > > HI Doug, > > > > Did you get the file I sent you? > > Any new idea about how I can fix the problem? > > > > Maryam > > > > On Tue, Apr 26, 2011 at 5:25 AM, Douglas Greve > > <greve(a)nmr.mgh.harvard.edu>wrote: > > > >> > >> The file will be found in $FREESURFER_HOME/fsfast/bin/mcparams2extreg, > >> but > >> until we figure out how to run matlab in a way that does not crash, it > >> will > >> not do any good to edit this file. Actually, can you send me your > >> version of > >> mcparams2extreg? I ran your matlab file on my mac by catting it to > >> matlab, > >> but it failed with I tried to run it with -r (don't know why). > >> > >> doug > >> > >> On 4/25/11 4:41 PM, Maryam Vaziri Pashkam wrote: > >> > >> Here is the m file. > >> > >> I have two versions of Matlab: R2008a, R2009b. The one that freesurfer > >> runs when calling matlab codes in 2009b. > >> > >> Sorry I am not sure what I should copy to my home directory and edit. I > >> thought the line you asked me to change was in the mcparams2extreg > >> file > >> which I don't know where it is. Could you explain a bit more? > >> > >> Maryam > >> > >> > >> > >> On Mon, Apr 25, 2011 at 4:34 PM, Douglas Greve > >> <greve(a)nmr.mgh.harvard.edu>wrote: > >> > >>> Can you send me the matlab file? And what version of matlab are you > >>> running? On the mac, you'll probably have to copy it to your home > >>> directly, > >>> edit it, then copy it back. When you copy it back, you'll have to sudo > >>> to > >>> get administrator privileges. > >>> > >>> doug > >>> > >>> > >>> On 4/25/11 4:26 PM, Maryam Vaziri Pashkam wrote: > >>> > >>> There is an error: > >>> > >>> ??? Error: Unexpected MATLAB operator when I run matlab -r > >>> matlabfile.m > >>> I wanted to change the mcparams2extreg to see if it works but I don't > >>> know > >>> how to change it and where it is located. > >>> > >>> Maryam > >>> > >>> On Mon, Apr 25, 2011 at 3:22 PM, Douglas Greve > >>> <greve(a)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(a)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(a)nmr.mgh.harvard.edu> wrote: > >>>>> > >>>>>> Send Freesurfer mailing list submissions to > >>>>>> freesurfer(a)nmr.mgh.harvard.edu > >>>>>> > >>>>>> To subscribe or unsubscribe via the World Wide Web, visit > >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>>>> or, via email, send a message with subject or body 'help' to > >>>>>> freesurfer-request(a)nmr.mgh.harvard.edu > >>>>>> > >>>>>> You can reach the person managing the list at > >>>>>> freesurfer-owner(a)nmr.mgh.harvard.edu > >>>>>> > >>>>>> When replying, please edit your Subject line so it is more specific > >>>>>> than "Re: Contents of Freesurfer digest..." > >>>>>> > >>>>>> > >>>>>> Today's Topics: > >>>>>> > >>>>>> 1. Fwd: error with motion correction (Maryam Vaziri Pashkam) > >>>>>> 2. Re: Fwd: error with motion correction (Douglas Greve) > >>>>>> > >>>>>> > >>>>>> > ---------------------------------------------------------------------- > >>>>>> > >>>>>> Message: 1 > >>>>>> Date: Sun, 24 Apr 2011 21:01:43 -0400 > >>>>>> From: Maryam Vaziri Pashkam <mvaziri.p(a)gmail.com> > >>>>>> Subject: [Freesurfer] Fwd: error with motion correction > >>>>>> To: freesurfer(a)nmr.mgh.harvard.edu > >>>>>> Message-ID: <BANLkTikkaJvqP5bxVD5e2moWQvwBrev9iA(a)mail.gmail.com> > >>>>>> Content-Type: text/plain; charset="iso-8859-1" > >>>>>> > >>>>>> Hi, > >>>>>> > >>>>>> I am running into trouble with motion correction on my Mac and > >>>>>> freesurfer > >>>>>> 4.5. > >>>>>> Originally I ran preproc-sess and got an error from mc-sess in the > >>>>>> part > >>>>>> (i > >>>>>> think) that runs the mcextreg. I ran mc-sess and the same error > >>>>>> happened (I > >>>>>> have copy pasted the log bellow). > >>>>>> It seems like the matlab program that runs mcparams2extreg cannot > >>>>>> read > >>>>>> the > >>>>>> fmc.mcdat file. when I did textread('fmc.mcdat') in matlab, I could > >>>>>> open the > >>>>>> file and it looked perfectly fine to me with the correct number of > >>>>>> TR's. > >>>>>> Any idea where the problem might be? > >>>>>> > >>>>>> Maryam > >>>>>> > >>>>>> preproc-sess -nosmooth -i f -sf sessid -df sessdir > >>>>>> -------------------------------------------------------------- > >>>>>> preproc-sess logfile is log/preproc-sess.log > >>>>>> -------------------------------------------------------------- > >>>>>> instem f > >>>>>> mc 1 f fmc > >>>>>> stc 0 fmc > >>>>>> sm 0 > >>>>>> mask 1 brain > >>>>>> 110419_xu_PDM1_02_PDM MC ----------------------------- > >>>>>> Sun Apr 24 20:42:29 EDT 2011 > >>>>>> /Users/maryam/mri-space/studies/PDM1/PDM1 > >>>>>> mc-sess -fstem f -fmcstem fmc -s 110419_xu_PDM1_02_PDM -d > >>>>>> /Users/maryam/mri-space/studies/PDM1/unpackdata -fsd bold -new > >>>>>> -update > >>>>>> -no-inorm > >>>>>> ---------------------------------------- > >>>>>> Logfile is > >>>>>> > >>>>>> > /Users/maryam/mri-space/studies/PDM1/PDM1/log/mc-110419_xu_PDM1_02_PDM-bold.log > >>>>>> ------------------------------------------- > >>>>>> > /Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM > >>>>>> RunList: 005 006 007 008 <005%20006%20007%20008> 011 012 013 014 > >>>>>> Targ Stem is 005/f > >>>>>> Update not needed > >>>>>> -rw-r--r-- 1 maryam staff 129203552 Apr 24 20:12 005/fmc.nii > >>>>>> -rw-r--r-- 1 maryam staff 64601952 Apr 24 19:12 005/f.nii > >>>>>> ------- ************************** ----------- > >>>>>> ------- Motion Correcting Run 006 ----------- > >>>>>> ------- ************************** ----------- > >>>>>> sess = 110419_xu_PDM1_02_PDM > >>>>>> Sun Apr 24 20:42:30 EDT 2011 > >>>>>> mc-afni2 --i 006/f.nii --t 005/f.nii --frame 0 --o 006/fmc.nii > >>>>>> --mcdat > >>>>>> 006/fmc.mcdat > >>>>>> > >>>>>> > /Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold > >>>>>> mri_info --nframes --o /tmp/mriinfo.2758 005/f.nii > >>>>>> log file is 006/fmc.nii.mclog > >>>>>> mcdat file is 006/fmc.mcdat > >>>>>> tmp dir is 006/tmp.mc-afni2.2758 > >>>>>> #@# -------------------------------- > >>>>>> > >>>>>> > /Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold > >>>>>> mri_convert 005/f.nii 006/tmp.mc-afni2.2758/tempvol.nii.gz --nskip 0 > >>>>>> --ndrop > >>>>>> 205 -odt float > >>>>>> mri_convert 005/f.nii 006/tmp.mc-afni2.2758/tempvol.nii.gz --nskip 0 > >>>>>> --ndrop > >>>>>> 205 -odt float > >>>>>> nskip = 0 > >>>>>> ndrop = 205 > >>>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > >>>>>> reading from 005/f.nii... > >>>>>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > >>>>>> i_ras = (-1, -0.000171665, -3.15037e-05) > >>>>>> j_ras = (0.000174532, -0.983572, -0.180519) > >>>>>> k_ras = (-2.07852e-18, -0.180519, 0.983572) > >>>>>> changing data type from 4 to 3 (noscale = 0)... > >>>>>> Dropping last 205 frames > >>>>>> writing to 006/tmp.mc-afni2.2758/tempvol.nii.gz... > >>>>>> #@# -------------------------------- > >>>>>> > >>>>>> > /Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold > >>>>>> mri_convert 006/f.nii 006/tmp.mc-afni2.2758/invol.nii.gz -odt float > >>>>>> mri_convert 006/f.nii 006/tmp.mc-afni2.2758/invol.nii.gz -odt float > >>>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > >>>>>> reading from 006/f.nii... > >>>>>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > >>>>>> i_ras = (-1, -0.000171665, -3.15037e-05) > >>>>>> j_ras = (0.000174532, -0.983572, -0.180519) > >>>>>> k_ras = (-2.07852e-18, -0.180519, 0.983572) > >>>>>> changing data type from 4 to 3 (noscale = 0)... > >>>>>> writing to 006/tmp.mc-afni2.2758/invol.nii.gz... > >>>>>> #@# -------------------------------- > >>>>>> > >>>>>> > /Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold > >>>>>> 3dvolreg -verbose -dfile 006/fmc.mcdat -base > >>>>>> 006/tmp.mc-afni2.2758/tempvol.nii.gz -prefix > >>>>>> 006/tmp.mc-afni2.2758/outvol.nii.gz > >>>>>> 006/tmp.mc-afni2.2758/invol.nii.gz > >>>>>> ++ 3dvolreg: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) > >>>>>> [32-bit] > >>>>>> ++ Authored by: RW Cox > >>>>>> *+ WARNING: If you are performing spatial transformations on an > >>>>>> oblique > >>>>>> dset, > >>>>>> such as 006/tmp.mc-afni2.2758/tempvol.nii.gz, > >>>>>> or viewing/combining it with volumes of differing obliquity, > >>>>>> you should consider running: > >>>>>> 3dWarp -deoblique > >>>>>> on this and other oblique datasets in the same session. > >>>>>> See 3dWarp -help for details. > >>>>>> ++ Oblique dataset:006/tmp.mc-afni2.2758/tempvol.nii.gz is 10.399981 > >>>>>> degrees > >>>>>> from plumb. > >>>>>> ++ Reading in base dataset 006/tmp.mc-afni2.2758/tempvol.nii.gz > >>>>>> ++ Oblique dataset:006/tmp.mc-afni2.2758/invol.nii.gz is 10.399981 > >>>>>> degrees > >>>>>> from plumb. > >>>>>> ++ Reading input dataset 006/tmp.mc-afni2.2758/invol.nii.gz > >>>>>> ++ Edging: x=4 y=4 z=2 > >>>>>> ++ Creating mask for -maxdisp > >>>>>> + Automask has 57667 voxels > >>>>>> + 10333 voxels left in -maxdisp mask after erosion > >>>>>> ++ Initializing alignment base > >>>>>> ++ Starting final pass on 206 sub-bricks: > >>>>>> > >>>>>> > 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205.. > >>>>>> ++ CPU time for realignment=16.6 s [=0.0808 s/sub-brick] > >>>>>> ++ Min : roll=-0.008 pitch=-0.103 yaw=-0.096 dS=+0.255 dL=-0.019 > >>>>>> dP=-0.151 > >>>>>> ++ Mean: roll=+0.031 pitch=-0.011 yaw=-0.045 dS=+0.619 dL=+0.037 > >>>>>> dP=-0.055 > >>>>>> ++ Max : roll=+0.060 pitch=+0.112 yaw=-0.010 dS=+0.693 dL=+0.075 > >>>>>> dP=+0.015 > >>>>>> ++ Max displacements (mm) for each sub-brick: > >>>>>> 0.49 0.65 0.63 0.74 0.69 0.75 0.71 0.77 0.70 0.76 0.67 0.77 0.72 > >>>>>> 0.73 > >>>>>> 0.66 > >>>>>> 0.67 0.67 0.67 0.69 0.70 0.72 0.66 0.71 0.68 0.72 0.67 0.73 0.68 > >>>>>> 0.73 > >>>>>> 0.66 > >>>>>> 0.73 0.66 0.70 0.64 0.72 0.69 0.71 0.71 0.72 0.66 0.66 0.67 0.72 > >>>>>> 0.70 > >>>>>> 0.71 > >>>>>> 0.72 0.71 0.69 0.72 0.72 0.71 0.72 0.72 0.69 0.71 0.74 0.73 0.69 > >>>>>> 0.72 > >>>>>> 0.72 > >>>>>> 0.76 0.76 0.79 0.73 0.75 0.74 0.75 0.75 0.71 0.74 0.67 0.72 0.65 > >>>>>> 0.72 > >>>>>> 0.65 > >>>>>> 0.69 0.69 0.65 0.68 0.64 0.72 0.67 0.67 0.68 0.69 0.65 0.73 0.67 > >>>>>> 0.71 > >>>>>> 0.69 > >>>>>> 0.73 0.72 0.76 0.74 0.72 0.66 0.68 0.69 0.69 0.68 0.68 0.70 0.73 > >>>>>> 0.70 > >>>>>> 0.73 > >>>>>> 0.78 0.74 0.73 0.75 0.74 0.72 0.74 0.63 0.66 0.68 0.74 0.72 0.74 > >>>>>> 0.79 > >>>>>> 0.74 > >>>>>> 0.74 0.76 0.79 0.79 0.74 0.76 0.70 0.75 0.72 0.78 0.74 0.78 0.76 > >>>>>> 0.80 > >>>>>> 0.76 > >>>>>> 0.79 0.77 0.76 0.76 0.75 0.73 0.80 0.78 0.81 0.78 0.84 0.76 0.79 > >>>>>> 0.77 > >>>>>> 0.79 > >>>>>> 0.76 0.83 0.77 0.79 0.77 0.84 0.76 0.80 0.77 0.81 0.72 0.79 0.74 > >>>>>> 0.80 > >>>>>> 0.77 > >>>>>> 0.83 0.81 0.82 0.76 0.81 0.75 0.78 0.74 0.75 0.71 0.75 0.73 0.77 > >>>>>> 0.77 > >>>>>> 0.80 > >>>>>> 0.77 0.80 0.75 0.73 0.77 0.72 0.76 0.72 0.76 0.72 0.72 0.69 0.66 > >>>>>> 0.68 > >>>>>> 0.65 > >>>>>> 0.68 0.64 0.70 0.62 0.70 0.62 0.69 0.67 0.74 0.75 0.74 > >>>>>> ++ Max displacement in automask = 0.84 (mm) at sub-brick 145 > >>>>>> ++ Wrote dataset to disk in 006/tmp.mc-afni2.2758/outvol.nii.gz > >>>>>> #@# -------------------------------- > >>>>>> > >>>>>> > /Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold > >>>>>> mri_convert 006/tmp.mc-afni2.2758/outvol.nii.gz 006/fmc.nii > >>>>>> --in_like > >>>>>> 005/f.nii > >>>>>> mri_convert 006/tmp.mc-afni2.2758/outvol.nii.gz 006/fmc.nii > >>>>>> --in_like > >>>>>> 005/f.nii > >>>>>> reading info from 005/f.nii... > >>>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > >>>>>> reading from 006/tmp.mc-afni2.2758/outvol.nii.gz... > >>>>>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > >>>>>> i_ras = (-1, -0.000171665, -3.15037e-05) > >>>>>> j_ras = (0.000174532, -0.983572, -0.180519) > >>>>>> k_ras = (-2.07852e-18, -0.180519, 0.983572) > >>>>>> writing to 006/fmc.nii... > >>>>>> ... cleaning up .... > >>>>>> Sun Apr 24 20:43:59 EDT 2011 > >>>>>> mc-afni2 done > >>>>>> INFO: Making external regressor from mc params > >>>>>> mcparams2extreg -mcfile 006/fmc.mcdat -northog 6 -extreg > >>>>>> 006/mcextreg > >>>>>> Logfile is 006/mcparams2extreg.log > >>>>>> ----------- Matlab file -------------- > >>>>>> mcfile = '006/fmc.mcdat'; > >>>>>> extreg = '006/mcextreg'; > >>>>>> nkeep = []; > >>>>>> northog = [6]; > >>>>>> pctorthog = []; > >>>>>> monly = 0; > >>>>>> > >>>>>> mc = textread(mcfile); > >>>>>> mc = mc(:,2:7); > >>>>>> ntrs = size(mc,1); > >>>>>> if(ntrs < 6) > >>>>>> fprintf('ERROR: ntrs = %d < 6\n',ntrs); > >>>>>> if(~monly) > >>>>>> fprintf('Quiting matlab\n'); > >>>>>> quit; > >>>>>> fprintf('should not be here\n'); > >>>>>> end > >>>>>> end > >>>>>> > >>>>>> if(~isempty(nkeep)) > >>>>>> x = mc(:,1:nkeep); > >>>>>> elseif(~isempty(northog)) > >>>>>> [u s v] = svd(mc); > >>>>>> ds = diag(s); > >>>>>> pct = 100*cumsum(ds)/sum(ds); > >>>>>> x = u(:,1:northog); > >>>>>> nkeep = northog; > >>>>>> fprintf('INFO: northog = %d, pct = %g\n',northog,pct(nkeep)); > >>>>>> else > >>>>>> [u s v] = svd(mc); > >>>>>> ds = diag(s); > >>>>>> pct = 100*cumsum(ds)/sum(ds); > >>>>>> nkeep = min(find(pct > pctorthog)); > >>>>>> x = u(:,1:nkeep); > >>>>>> fprintf('INFO: pctorthog = %g, nkeep = %d\n',pctorthog,nkeep); > >>>>>> end > >>>>>> > >>>>>> x2 = zeros(1,1,nkeep,ntrs); > >>>>>> x2(1,1,:,:) = x'; %' > >>>>>> %fmri_svbvolume(x2,extreg); > >>>>>> > >>>>>> mri.vol = permute(x2,[1 3 2 4]); > >>>>>> mri.tr = 0; > >>>>>> mri.flip_angle = 0; > >>>>>> mri.te = 0; > >>>>>> mri.ti = 0; > >>>>>> mri.vox2ras0 = eye(4); > >>>>>> mri.xsize = 1; > >>>>>> mri.ysize = 1; > >>>>>> mri.zsize = 1; > >>>>>> mri.volres = [1 1 1]; > >>>>>> mri.volsize = [size(mri.vol,1) size(mri.vol,2) size(mri.vol,3)]; > >>>>>> fname = sprintf('%s.bhdr',extreg); > >>>>>> MRIwrite(mri,fname); > >>>>>> > >>>>>> quit; > >>>>>> > >>>>>> ----------------------------------- > >>>>>> ------------------------------------------ > >>>>>> ------- matlab output -------------------- > >>>>>> Warning: Unable to open display 'iconic'. You will not be able to > >>>>>> display > >>>>>> graphics on the screen. > >>>>>> > >>>>>> < M A T L A B (R) > > >>>>>> Copyright 1984-2009 The MathWorks, Inc. > >>>>>> Version 7.9.0.529 (R2009b) 64-bit (maci64) > >>>>>> August 12, 2009 > >>>>>> > >>>>>> To get started, type one of these: helpwin, helpdesk, or demo. > >>>>>> For product information, visit www.mathworks.com. > >>>>>> > >>>>>> >> >> >> >> >> >> >> >> ??? Error using ==> textread at 167 > >>>>>> File not found. > >>>>>> > >>>>>> >> ??? Undefined variable mc. > >>>>>> > >>>>>> >> ??? Undefined function or variable 'mc'. > >>>>>> > >>>>>> >> ??? Undefined function or variable 'ntrs'. > >>>>>> > >>>>>> >> >> ??? Undefined function or variable 'mc'. > >>>>>> > >>>>>> >> >> ??? Undefined function or variable 'ntrs'. > >>>>>> > >>>>>> >> ??? Undefined function or variable 'x'. > >>>>>> > >>>>>> >> >> >> ??? Undefined function or variable 'x2'. > >>>>>> > >>>>>> >> >> >> >> >> >> >> >> >> >> ??? Reference to non-existent field > >>>>>> 'vol'. > >>>>>> > >>>>>> >> >> ??? Reference to non-existent field 'vol'. > >>>>>> > >>>>>> Error in ==> MRIwrite at 70 > >>>>>> bmri.voldim = [size(mri.vol,1) size(mri.vol,2) size(mri.vol,3)]; > >>>>>> > >>>>>> >> >> ------------------------------------------ > >>>>>> ERROR: output not created > >>>>>> ERROR: mc-sess failed > >>>>>>

1 0

tksurfer tcl script
by Yang Liu 28 Apr '11

28 Apr '11

Hi all, I want to save the tiffs of different views automatically. I am trying to use tcl script to do it. My problem is that I need to pass the file's name that is being displayed in the tksurfer window to the tiff file that I want to save to. For example, I am running tksurfer -f $surface_file -tcl my_script.tcl In my_script.tcl, I have the following command: save_tiff ${file_name}-lateral.tiff How can I pass the $surface_file in my command to ${file_name} in my_scripts.tcl? Thanks. Yang

3 3

general question on use of optseq2
by maya visser 28 Apr '11

28 Apr '11

Hi all, I have a very general question and hope someone can help. I would like to use optseq2 to optimise my fMRI design. I will use a event-related parametric design. I will have 2 conditions with each 4 loads. Will I define only 2 conditions/events in optseq as I will investigate the load variation within these two conditions. Or is it better to define 8 events? Thanks in advance, Maya

1 0

DTI Paramters
by Peter J. Molfese 27 Apr '11

27 Apr '11

Hello, We're gearing up for a new study and planning to collect DTI data along with both functional and anatomical data. Is there a particular protocol that Freesurfer (and Tracula) will work best with? I found the suggested sequences for anatomical reconstruction, but didn't see any for DTI specifically. Also, any idea when version 5.1 will be out of beta? Thanks, Peter J. Molfese, Ph.D. Postdoctoral Associate Haskins Laboratories 300 George Street, Suite 900 New Haven, CT 06511 peter.molfese(a)yale.edu

1 0

Re: [Freesurfer] Freesurfer Digest, Vol 86, Issue 77
by Maryam Vaziri Pashkam 27 Apr '11

27 Apr '11

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(a)nmr.mgh.harvard.edu>wrote: > > The file will be found in $FREESURFER_HOME/fsfast/bin/mcparams2extreg, but > until we figure out how to run matlab in a way that does not crash, it will > not do any good to edit this file. Actually, can you send me your version of > mcparams2extreg? I ran your matlab file on my mac by catting it to matlab, > but it failed with I tried to run it with -r (don't know why). > > doug > > On 4/25/11 4:41 PM, Maryam Vaziri Pashkam wrote: > > Here is the m file. > > I have two versions of Matlab: R2008a, R2009b. The one that freesurfer > runs when calling matlab codes in 2009b. > > Sorry I am not sure what I should copy to my home directory and edit. I > thought the line you asked me to change was in the mcparams2extreg file > which I don't know where it is. Could you explain a bit more? > > Maryam > > > > On Mon, Apr 25, 2011 at 4:34 PM, Douglas Greve <greve(a)nmr.mgh.harvard.edu>wrote: > >> Can you send me the matlab file? And what version of matlab are you >> running? On the mac, you'll probably have to copy it to your home directly, >> edit it, then copy it back. When you copy it back, you'll have to sudo to >> get administrator privileges. >> >> doug >> >> >> On 4/25/11 4:26 PM, Maryam Vaziri Pashkam wrote: >> >> There is an error: >> >> ??? Error: Unexpected MATLAB operator when I run matlab -r matlabfile.m >> I wanted to change the mcparams2extreg to see if it works but I don't know >> how to change it and where it is located. >> >> Maryam >> >> On Mon, Apr 25, 2011 at 3:22 PM, Douglas Greve <greve(a)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(a)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(a)nmr.mgh.harvard.edu> wrote: >>>> >>>>> Send Freesurfer mailing list submissions to >>>>> freesurfer(a)nmr.mgh.harvard.edu >>>>> >>>>> To subscribe or unsubscribe via the World Wide Web, visit >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> or, via email, send a message with subject or body 'help' to >>>>> freesurfer-request(a)nmr.mgh.harvard.edu >>>>> >>>>> You can reach the person managing the list at >>>>> freesurfer-owner(a)nmr.mgh.harvard.edu >>>>> >>>>> When replying, please edit your Subject line so it is more specific >>>>> than "Re: Contents of Freesurfer digest..." >>>>> >>>>> >>>>> Today's Topics: >>>>> >>>>> 1. Fwd: error with motion correction (Maryam Vaziri Pashkam) >>>>> 2. Re: Fwd: error with motion correction (Douglas Greve) >>>>> >>>>> >>>>> ---------------------------------------------------------------------- >>>>> >>>>> Message: 1 >>>>> Date: Sun, 24 Apr 2011 21:01:43 -0400 >>>>> From: Maryam Vaziri Pashkam <mvaziri.p(a)gmail.com> >>>>> Subject: [Freesurfer] Fwd: error with motion correction >>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>> Message-ID: <BANLkTikkaJvqP5bxVD5e2moWQvwBrev9iA(a)mail.gmail.com> >>>>> Content-Type: text/plain; charset="iso-8859-1" >>>>> >>>>> Hi, >>>>> >>>>> I am running into trouble with motion correction on my Mac and >>>>> freesurfer >>>>> 4.5. >>>>> Originally I ran preproc-sess and got an error from mc-sess in the part >>>>> (i >>>>> think) that runs the mcextreg. I ran mc-sess and the same error >>>>> happened (I >>>>> have copy pasted the log bellow). >>>>> It seems like the matlab program that runs mcparams2extreg cannot read >>>>> the >>>>> fmc.mcdat file. when I did textread('fmc.mcdat') in matlab, I could >>>>> open the >>>>> file and it looked perfectly fine to me with the correct number of >>>>> TR's. >>>>> Any idea where the problem might be? >>>>> >>>>> Maryam >>>>> >>>>> preproc-sess -nosmooth -i f -sf sessid -df sessdir >>>>> -------------------------------------------------------------- >>>>> preproc-sess logfile is log/preproc-sess.log >>>>> -------------------------------------------------------------- >>>>> instem f >>>>> mc 1 f fmc >>>>> stc 0 fmc >>>>> sm 0 >>>>> mask 1 brain >>>>> 110419_xu_PDM1_02_PDM MC ----------------------------- >>>>> Sun Apr 24 20:42:29 EDT 2011 >>>>> /Users/maryam/mri-space/studies/PDM1/PDM1 >>>>> mc-sess -fstem f -fmcstem fmc -s 110419_xu_PDM1_02_PDM -d >>>>> /Users/maryam/mri-space/studies/PDM1/unpackdata -fsd bold -new -update >>>>> -no-inorm >>>>> ---------------------------------------- >>>>> Logfile is >>>>> >>>>> /Users/maryam/mri-space/studies/PDM1/PDM1/log/mc-110419_xu_PDM1_02_PDM-bold.log >>>>> ------------------------------------------- >>>>> /Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM >>>>> RunList: 005 006 007 008 <005%20006%20007%20008> 011 012 013 014 >>>>> Targ Stem is 005/f >>>>> Update not needed >>>>> -rw-r--r-- 1 maryam staff 129203552 Apr 24 20:12 005/fmc.nii >>>>> -rw-r--r-- 1 maryam staff 64601952 Apr 24 19:12 005/f.nii >>>>> ------- ************************** ----------- >>>>> ------- Motion Correcting Run 006 ----------- >>>>> ------- ************************** ----------- >>>>> sess = 110419_xu_PDM1_02_PDM >>>>> Sun Apr 24 20:42:30 EDT 2011 >>>>> mc-afni2 --i 006/f.nii --t 005/f.nii --frame 0 --o 006/fmc.nii --mcdat >>>>> 006/fmc.mcdat >>>>> >>>>> /Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold >>>>> mri_info --nframes --o /tmp/mriinfo.2758 005/f.nii >>>>> log file is 006/fmc.nii.mclog >>>>> mcdat file is 006/fmc.mcdat >>>>> tmp dir is 006/tmp.mc-afni2.2758 >>>>> #@# -------------------------------- >>>>> >>>>> /Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold >>>>> mri_convert 005/f.nii 006/tmp.mc-afni2.2758/tempvol.nii.gz --nskip 0 >>>>> --ndrop >>>>> 205 -odt float >>>>> mri_convert 005/f.nii 006/tmp.mc-afni2.2758/tempvol.nii.gz --nskip 0 >>>>> --ndrop >>>>> 205 -odt float >>>>> nskip = 0 >>>>> ndrop = 205 >>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ >>>>> reading from 005/f.nii... >>>>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 >>>>> i_ras = (-1, -0.000171665, -3.15037e-05) >>>>> j_ras = (0.000174532, -0.983572, -0.180519) >>>>> k_ras = (-2.07852e-18, -0.180519, 0.983572) >>>>> changing data type from 4 to 3 (noscale = 0)... >>>>> Dropping last 205 frames >>>>> writing to 006/tmp.mc-afni2.2758/tempvol.nii.gz... >>>>> #@# -------------------------------- >>>>> >>>>> /Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold >>>>> mri_convert 006/f.nii 006/tmp.mc-afni2.2758/invol.nii.gz -odt float >>>>> mri_convert 006/f.nii 006/tmp.mc-afni2.2758/invol.nii.gz -odt float >>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ >>>>> reading from 006/f.nii... >>>>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 >>>>> i_ras = (-1, -0.000171665, -3.15037e-05) >>>>> j_ras = (0.000174532, -0.983572, -0.180519) >>>>> k_ras = (-2.07852e-18, -0.180519, 0.983572) >>>>> changing data type from 4 to 3 (noscale = 0)... >>>>> writing to 006/tmp.mc-afni2.2758/invol.nii.gz... >>>>> #@# -------------------------------- >>>>> >>>>> /Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold >>>>> 3dvolreg -verbose -dfile 006/fmc.mcdat -base >>>>> 006/tmp.mc-afni2.2758/tempvol.nii.gz -prefix >>>>> 006/tmp.mc-afni2.2758/outvol.nii.gz 006/tmp.mc-afni2.2758/invol.nii.gz >>>>> ++ 3dvolreg: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) [32-bit] >>>>> ++ Authored by: RW Cox >>>>> *+ WARNING: If you are performing spatial transformations on an >>>>> oblique >>>>> dset, >>>>> such as 006/tmp.mc-afni2.2758/tempvol.nii.gz, >>>>> or viewing/combining it with volumes of differing obliquity, >>>>> you should consider running: >>>>> 3dWarp -deoblique >>>>> on this and other oblique datasets in the same session. >>>>> See 3dWarp -help for details. >>>>> ++ Oblique dataset:006/tmp.mc-afni2.2758/tempvol.nii.gz is 10.399981 >>>>> degrees >>>>> from plumb. >>>>> ++ Reading in base dataset 006/tmp.mc-afni2.2758/tempvol.nii.gz >>>>> ++ Oblique dataset:006/tmp.mc-afni2.2758/invol.nii.gz is 10.399981 >>>>> degrees >>>>> from plumb. >>>>> ++ Reading input dataset 006/tmp.mc-afni2.2758/invol.nii.gz >>>>> ++ Edging: x=4 y=4 z=2 >>>>> ++ Creating mask for -maxdisp >>>>> + Automask has 57667 voxels >>>>> + 10333 voxels left in -maxdisp mask after erosion >>>>> ++ Initializing alignment base >>>>> ++ Starting final pass on 206 sub-bricks: >>>>> >>>>> 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205.. >>>>> ++ CPU time for realignment=16.6 s [=0.0808 s/sub-brick] >>>>> ++ Min : roll=-0.008 pitch=-0.103 yaw=-0.096 dS=+0.255 dL=-0.019 >>>>> dP=-0.151 >>>>> ++ Mean: roll=+0.031 pitch=-0.011 yaw=-0.045 dS=+0.619 dL=+0.037 >>>>> dP=-0.055 >>>>> ++ Max : roll=+0.060 pitch=+0.112 yaw=-0.010 dS=+0.693 dL=+0.075 >>>>> dP=+0.015 >>>>> ++ Max displacements (mm) for each sub-brick: >>>>> 0.49 0.65 0.63 0.74 0.69 0.75 0.71 0.77 0.70 0.76 0.67 0.77 0.72 0.73 >>>>> 0.66 >>>>> 0.67 0.67 0.67 0.69 0.70 0.72 0.66 0.71 0.68 0.72 0.67 0.73 0.68 0.73 >>>>> 0.66 >>>>> 0.73 0.66 0.70 0.64 0.72 0.69 0.71 0.71 0.72 0.66 0.66 0.67 0.72 0.70 >>>>> 0.71 >>>>> 0.72 0.71 0.69 0.72 0.72 0.71 0.72 0.72 0.69 0.71 0.74 0.73 0.69 0.72 >>>>> 0.72 >>>>> 0.76 0.76 0.79 0.73 0.75 0.74 0.75 0.75 0.71 0.74 0.67 0.72 0.65 0.72 >>>>> 0.65 >>>>> 0.69 0.69 0.65 0.68 0.64 0.72 0.67 0.67 0.68 0.69 0.65 0.73 0.67 0.71 >>>>> 0.69 >>>>> 0.73 0.72 0.76 0.74 0.72 0.66 0.68 0.69 0.69 0.68 0.68 0.70 0.73 0.70 >>>>> 0.73 >>>>> 0.78 0.74 0.73 0.75 0.74 0.72 0.74 0.63 0.66 0.68 0.74 0.72 0.74 0.79 >>>>> 0.74 >>>>> 0.74 0.76 0.79 0.79 0.74 0.76 0.70 0.75 0.72 0.78 0.74 0.78 0.76 0.80 >>>>> 0.76 >>>>> 0.79 0.77 0.76 0.76 0.75 0.73 0.80 0.78 0.81 0.78 0.84 0.76 0.79 0.77 >>>>> 0.79 >>>>> 0.76 0.83 0.77 0.79 0.77 0.84 0.76 0.80 0.77 0.81 0.72 0.79 0.74 0.80 >>>>> 0.77 >>>>> 0.83 0.81 0.82 0.76 0.81 0.75 0.78 0.74 0.75 0.71 0.75 0.73 0.77 0.77 >>>>> 0.80 >>>>> 0.77 0.80 0.75 0.73 0.77 0.72 0.76 0.72 0.76 0.72 0.72 0.69 0.66 0.68 >>>>> 0.65 >>>>> 0.68 0.64 0.70 0.62 0.70 0.62 0.69 0.67 0.74 0.75 0.74 >>>>> ++ Max displacement in automask = 0.84 (mm) at sub-brick 145 >>>>> ++ Wrote dataset to disk in 006/tmp.mc-afni2.2758/outvol.nii.gz >>>>> #@# -------------------------------- >>>>> >>>>> /Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold >>>>> mri_convert 006/tmp.mc-afni2.2758/outvol.nii.gz 006/fmc.nii --in_like >>>>> 005/f.nii >>>>> mri_convert 006/tmp.mc-afni2.2758/outvol.nii.gz 006/fmc.nii --in_like >>>>> 005/f.nii >>>>> reading info from 005/f.nii... >>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ >>>>> reading from 006/tmp.mc-afni2.2758/outvol.nii.gz... >>>>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 >>>>> i_ras = (-1, -0.000171665, -3.15037e-05) >>>>> j_ras = (0.000174532, -0.983572, -0.180519) >>>>> k_ras = (-2.07852e-18, -0.180519, 0.983572) >>>>> writing to 006/fmc.nii... >>>>> ... cleaning up .... >>>>> Sun Apr 24 20:43:59 EDT 2011 >>>>> mc-afni2 done >>>>> INFO: Making external regressor from mc params >>>>> mcparams2extreg -mcfile 006/fmc.mcdat -northog 6 -extreg 006/mcextreg >>>>> Logfile is 006/mcparams2extreg.log >>>>> ----------- Matlab file -------------- >>>>> mcfile = '006/fmc.mcdat'; >>>>> extreg = '006/mcextreg'; >>>>> nkeep = []; >>>>> northog = [6]; >>>>> pctorthog = []; >>>>> monly = 0; >>>>> >>>>> mc = textread(mcfile); >>>>> mc = mc(:,2:7); >>>>> ntrs = size(mc,1); >>>>> if(ntrs < 6) >>>>> fprintf('ERROR: ntrs = %d < 6\n',ntrs); >>>>> if(~monly) >>>>> fprintf('Quiting matlab\n'); >>>>> quit; >>>>> fprintf('should not be here\n'); >>>>> end >>>>> end >>>>> >>>>> if(~isempty(nkeep)) >>>>> x = mc(:,1:nkeep); >>>>> elseif(~isempty(northog)) >>>>> [u s v] = svd(mc); >>>>> ds = diag(s); >>>>> pct = 100*cumsum(ds)/sum(ds); >>>>> x = u(:,1:northog); >>>>> nkeep = northog; >>>>> fprintf('INFO: northog = %d, pct = %g\n',northog,pct(nkeep)); >>>>> else >>>>> [u s v] = svd(mc); >>>>> ds = diag(s); >>>>> pct = 100*cumsum(ds)/sum(ds); >>>>> nkeep = min(find(pct > pctorthog)); >>>>> x = u(:,1:nkeep); >>>>> fprintf('INFO: pctorthog = %g, nkeep = %d\n',pctorthog,nkeep); >>>>> end >>>>> >>>>> x2 = zeros(1,1,nkeep,ntrs); >>>>> x2(1,1,:,:) = x'; %' >>>>> %fmri_svbvolume(x2,extreg); >>>>> >>>>> mri.vol = permute(x2,[1 3 2 4]); >>>>> mri.tr = 0; >>>>> mri.flip_angle = 0; >>>>> mri.te = 0; >>>>> mri.ti = 0; >>>>> mri.vox2ras0 = eye(4); >>>>> mri.xsize = 1; >>>>> mri.ysize = 1; >>>>> mri.zsize = 1; >>>>> mri.volres = [1 1 1]; >>>>> mri.volsize = [size(mri.vol,1) size(mri.vol,2) size(mri.vol,3)]; >>>>> fname = sprintf('%s.bhdr',extreg); >>>>> MRIwrite(mri,fname); >>>>> >>>>> quit; >>>>> >>>>> ----------------------------------- >>>>> ------------------------------------------ >>>>> ------- matlab output -------------------- >>>>> Warning: Unable to open display 'iconic'. You will not be able to >>>>> display >>>>> graphics on the screen. >>>>> >>>>> < M A T L A B (R) > >>>>> Copyright 1984-2009 The MathWorks, Inc. >>>>> Version 7.9.0.529 (R2009b) 64-bit (maci64) >>>>> August 12, 2009 >>>>> >>>>> To get started, type one of these: helpwin, helpdesk, or demo. >>>>> For product information, visit www.mathworks.com. >>>>> >>>>> >> >> >> >> >> >> >> >> ??? Error using ==> textread at 167 >>>>> File not found. >>>>> >>>>> >> ??? Undefined variable mc. >>>>> >>>>> >> ??? Undefined function or variable 'mc'. >>>>> >>>>> >> ??? Undefined function or variable 'ntrs'. >>>>> >>>>> >> >> ??? Undefined function or variable 'mc'. >>>>> >>>>> >> >> ??? Undefined function or variable 'ntrs'. >>>>> >>>>> >> ??? Undefined function or variable 'x'. >>>>> >>>>> >> >> >> ??? Undefined function or variable 'x2'. >>>>> >>>>> >> >> >> >> >> >> >> >> >> >> ??? Reference to non-existent field >>>>> 'vol'. >>>>> >>>>> >> >> ??? Reference to non-existent field 'vol'. >>>>> >>>>> Error in ==> MRIwrite at 70 >>>>> bmri.voldim = [size(mri.vol,1) size(mri.vol,2) size(mri.vol,3)]; >>>>> >>>>> >> >> ------------------------------------------ >>>>> ERROR: output not created >>>>> ERROR: mc-sess failed >>>>>

1 0

Unknown label in Parcellation
by Pedro Paulo de Magalhães Oliveira Junior 27 Apr '11

27 Apr '11

In one study we are conducting we found significant difference in cortical thickness between the two groups in some areas. One of those areas are lh_unknown. Is this an error or it's a still unlabelled area? thanks Pedro Paulo Jr

3 4

Re: [Freesurfer] about mri_vol2surf
by greve＠nmr.mgh.harvard.edu 27 Apr '11

27 Apr '11

> > Hi Doug: > > When you talk about zero out subcortical region, when does this zero > out happen? it should happen after register vertex into functional > space, right? Then it happens before functional space interpolation > or after interpolation? It happens after interpolation. > > And one more question about the register.dat file used for this > process. whose resolution info is used in register.dat file ? the low > resolution functional image (moving image) or high resolution anatomy > image? Is the resolution of fsaverage is 2mm*2mm*0.15mm? The low resolution (though those numbers are no longer used internally -- the resolution is obtained from the mov volume). doug > > Thanks much! > > Jing > > Date: Tue, 26 Apr 2011 17:11:45 -0400 > From: greve(a)nmr.mgh.harvard.edu > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] about mri_vol2surf > > > > > > > > > > Hi Jing, by default it does include all the non-cortical structures > in the medial wall, including any subcortical structures. If you > include --cortex in the command-line it zeros them out. The way it > works is that it goes through each vertex on the surface, gets the > RAS coordinate for that vertex, applies the registration matrix to > map it into the function space, then samples the function value > using nearest neighbor (can change to trilinear with --interp > trilin). > > > > doug > > > > On 4/26/11 1:51 PM, Jing Ming wrote: > > > Hi Surfers: > > > > I am using mri_vol2surf to project fMRI result into the > fsaverage surface. And the fMRI result may contain some > subcortical regions, so, I wonder mri_vol2surf will automatically > get rid of the subcortical region and only map cortical area into > surface right? Is there any material about the mapping algorithm > of mri_vol2surf? Thanks much! > > > > Jing > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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.

1 0

GroupAnaysis Tutorial question: GLM directory error
by Carl Anderson 27 Apr '11

27 Apr '11

Dear Freesurfer, My current subjects dir is: /Applications/freesurfer/subjects/buckner_data/tutorial_subjs/group_analysis_tutorial When I run the following (from the tutorial): mri_glmfit-sim --glmdir lh.gender_age.glmdir --sim mc-z 5 4 mc-z.negative --sim-sign neg --overwrite I get the following error: ERROR: cannot find /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/group_analysis_tutorial/glm I tried the following: mri_glmfit-sim --glmdir /Applications/freesurfer/subjects/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.glmdir --sim mc-z 5 4 mc-z.negative --sim-sign neg --overwrite With the same result. Any suggestions? Thanks! -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

1 0

wrong sagittal orientation
by Saad Ramadan 27 Apr '11

27 Apr '11

Hi all, Upon creating my .nii file from my Siemens MPRAGE data using mri_convert, and opening nii file in freesurfer, I notice that the sagital view has the wrong orientation. What I mean is that on teh scanner I can see nose on left side of image, but on freesurfer I see nose on right. I am using mri-convert with no options. Is thsi normal or am doing anything wrong? Thanks in advance.

3 2

qdec analysis different scanner
by John Fredy 27 Apr '11

27 Apr '11

Hello all, In voxel based morphometry is not recommended use images from different scanners. This recommendation also apply in the qdec analysis? Thanks in advance John Ochoa Universidad de Antioquia Instituto Neurológico de Antioquia

2 1

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Freesurfer April 2011