Freesurfer April 2011

freesurfer@nmr.mgh.harvard.edu

121 participants
166 discussions

Re: [Freesurfer] high resolution segmentation
by Bruce Fischl 26 Apr '11

26 Apr '11

Hi Jon, I'll leave this to Krish, as he's the local expert on mris_volmask, but it definitely could. Do you want to upload an example of a subject that failed for us to try out? Bruce On Thu, 14 Apr 2011, Jonathan Winawer wrote: > Hmm. At least when I use tkmedit, the surfaces seem to be correctly > registered to both the high resolution volume (rawavg.mgz) and the 1x1x1 > volume (T1.mgz). So it does not look like a coordinate problem, at least to > my un-expert eyes. But maybe tkmedit does a different transform of the > surfaces than mris_volmask? > > In any case, the failure of mris_volmask to produce a good ribbon file > follows a very characteristic pattern that looks more like a topology > confusion to me, as you can see in the attached png. I say this because > voxels along the gray-white border are labeled white (with some gaps) and > voxels along the pial surface are labeled as gray. Also, some of the regions > which are unlabeled holes in the correct (original) ribbon become labeled > islands in the new, high-res ribbon. So it looks like the surfaces are in the > right place, but they are somehow not filled in correctly. This precise > pattern happens with every high-resolution brain I use when I try to re-run > mris_volmask. In contrast when I rerun mris_volmask on bert, it works > perfectly, though in this case the rawavg.mgz is already registered to T1.mgz > and has the same resolution. > > Could a coordinate problem cause this? > > Sorry for all the questions. I seem to be stuck though. Many thanks again > for your quick responses! > > Jon > >

2 4

recon-all error
by Yunjo Lee 26 Apr '11

26 Apr '11

Dear FreeSurfer experts, I just installed FreeSurfer in a virtual machine (Ubuntu) and ran recon-all. I kept getting the following error message. Could you advise? Thanks in advance, Yunjo *Here's the error message:* 0597: dt=0.056000, rms=0.417 (0.032%), neg=0, invalid=766 0598: dt=0.028000, rms=0.417 (-0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22111.002 ms 0599: dt=0.000000, rms=0.417 (0.000%), neg=0, invalid=766 GCAMwrite(transforms/talairach.m3z): gzip encountered error. writing output transformation to transforms/talairach.m3z... mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Tue Apr 26 16:21:09 EDT 2011 /usr/local/freesurfer/subjects/YC7178/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux VMBronzeWing 2.6.35-22-generic #33-Ubuntu SMP Sun Sep 19 20:34:50 UTC 2010 i686 GNU/Linux recon-all -s YC7178 exited with ERRORS at Tue Apr 26 16:21:14 EDT 2011

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about mri_vol2surf
by Jing Ming 26 Apr '11

26 Apr '11

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

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Comparison between two hemispheres using QDEC.
by Krista Kelly 26 Apr '11

26 Apr '11

I'm using QDEC to analyze cortical thickness of a patient population compared to controls. One of the things I wanted to analyze is the difference between hemispheres within patients. It seems that I can only analyze one hemisphere at a time in QDEC; is there any way to analyze the difference BETWEEN hemispheres for one group? Thank you!

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(no subject)
by kevin bickart 26 Apr '11

26 Apr '11

Hi all, I am interested in projecting my functional connectivity z map to the cortical surface. I attempted to use mri_vol2surf but received a warning message (see command and output below) indicating that the voxel resolution in the source volume doesn't match the registration file. Perhaps as a result of this, when I attempt to load the resulting .mgh file in tksurfer, nothing appears on the cortical surface image. Any idea what went wrong? Thanks in advance, Kevin Here's the my command and output: mri_vol2surf --mov N89_L_WholeAmyMask_g7_zfrm_avg.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --hemi lh --trgsubject fsaverage --out lh.L_WholeAmy_buckner_YC.mgh --projfrac 1 --surf-fwhm 4 srcvol = N89_L_WholeAmyMask_g7_zfrm_avg.nii.gz srcreg = /usr/local/freesurfer/stable5_0_0/average/mni152.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 1 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume WARNING: the voxel resolution in the source volume (2,2,2) differs from that listed in the registration file (1,1,1) Reading surface /space/sake/3/users/inverse/subjects/fsaverage/surf/lh.white Done reading source surface Reading thickness /space/sake/3/users/inverse/subjects/fsaverage/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 1 1 1 using old Done mapping volume to surface Number of source voxels hit = 23569 Surface smoothing by fwhm = 4 (n=12) Writing to lh.L_WholeAmy_buckner_YC.mgh Dim: 163842 1 1 -- Kevin Bickart MD-PhD Student Department of Anatomy and Neurobiology Boston University School of Medicine live UP to it

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display issue on MacBook Pro 13"
by Ilana Hairston 26 Apr '11

26 Apr '11

Hi there, I'm traveling and using my laptop for freesurfer. For some reason the displayed windows are greater than my screen (at least for tksurfer), leaving boxes such as FDR correction, Apply outside range. I'm using the highest possible resolution. Is there something that can be adjusted on X11 or the terminal to fix this? Thanks Ilana

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Re: [Freesurfer] Freesurfer Digest, Vol 86, Issue 77
by Maryam Vaziri Pashkam 26 Apr '11

26 Apr '11

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: 005 006 007 008 011 012 013 014 > 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 >

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V1 labels registration
by Michael Thomas Smith 26 Apr '11

26 Apr '11

Hello, I'm trying to use the V1 localisation tool provided by Hinds et al[1]. I've found the voxels labelled don't appear to be aligned correctly. The code I ran to do this follows: First the symbolic link and running the tool: $ ln -sf ~/V1_average ~/fs_subjects/ $ ~/V1_average/scripts/predict_v1.sh s01 Then I used tkmedit to view the result, comparing to the both T1.mgz or orig.mgz. E.g. $ tkmedit s01 T1.mgz then chose File->Label->Load label and selected "lh.v1.predict.label": http://www.sal.mvm.ed.ac.uk/images/v1_tkmedit.png I thought maybe this could be because of not realigning the image or some such. I thought I could try looking at the image once converted to nifty format: $ mri_convert -rl mri/T1.mgz -rt nearest mri/T1.mgz ~/Desktop/temp.nii $ mri_label2vol --label label/rh.v1.prob.label --regheader ~/Desktop/temp.nii --temp ~/Desktop/temp.nii --o ~/Desktop/test.nii However it still looks wrong: http://www.sal.mvm.ed.ac.uk/images/v1_nii.png Any ideas on what I'm doing wrong in the V1 localisation? Thanks for any advice, Mike Smith [1] http://surfer.nmr.mgh.harvard.edu/fswiki/V1 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

2 1

about recon-all
by Xiaoying Tang 26 Apr '11

26 Apr '11

Hi All,I find the following content on the wikipage of freesurfer: Q. I have already skull-stripped data. Can I submit it to recon-all? A: If your skull-stripped volume does not have the cerebellum, then no. If it does, then yes, however you will have to run the data a bit differently. First you must run only -autorecon1 like this: *recon-all -autorecon1 -noskullstrip -s <subjid>* Then you will have to make a symbolic link or copy T1.mgz to brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz. Finally, open this brainmask.mgz file and check that it looks okay (there is no skull, cerebellum is intact; use the sample subject *bert* that comes with your FreeSurfer installation to make sure it looks comparable). From there you can run the final stages of recon-all: *recon-all -autrecon1 -autorecon3 -s <subjid> I am a little confused: should the final stages be "recon-all -autorecon2 -autorecon3 -s **<subjid>" since we have already run the -autorecon1 via **"recon-all -autorecon1 -noskullstrip -s <subjid>"? Thanks a lot for your answering. Best, Xiaoying Tang*

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two questions about qdec
by liyari5018 25 Apr '11

25 Apr '11

Hi all, I have two questions about QDEC: 1\Is there anyway to auto (not manually draw ROI) extract information (include area, the max p-value, the num of vertexes) from the significant different area? Or how can I extract the information quickly? 2\Is the coordinates in qdec belong to 'Talairach' coordinates system? I'm confused with the coordinates. I will appreciate for you reply! Best, lee

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Freesurfer April 2011