Freesurfer December 2010

freesurfer@nmr.mgh.harvard.edu

92 participants
128 discussions

looking for load dependent effects - task regressors?
by Katie Bettencourt 02 Dec '10

02 Dec '10

Hi all, I was running an event-related analysis where the number of targets change, and I would really like to find an area that tracks their behavioral performance so that it would increase as set size increases, but then level off when performance does. Basically I have 5 set sizes, 1,2,3,4,6 items. performance increases to set size 4 then plateaus. And I want to find an area of the brain that reflects this same pattern. For now, I've been looking at areas that are more active for the higher set sizes than lower ones, but I'd really like to weight the set sizes by their performance so that where performance is flat, we'd see flat activity too. Does that make sense? I see that in Freesurfer version 5 you can use external task regressors, is that what I want to use? And if so, how do I do that? Is there any way to do this in version 4.5? Katie

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Re: [Freesurfer] selxavg-sess vs selxavg3-sess
by Katie Bettencourt 02 Dec '10

02 Dec '10

Hi all, I'm still trying to sort out some problems I've been having with selxavg3-sess in Freesurfer 4.5 on RedHat Linux, CentOs 5.5. I've tried a bunch of things, but I will provide the simplified process here as a starting point. I have a blocked design where I have 3 conditions, fixation, noise, and shape. Things look good when I compare shape vs noise, but very very bad in an unrealistic way when I compare anything to fixation (shape vs fixation, noise vs fixation, active vs fixation). Attached are the pictures I get. The subjects are not moving much (checked the motion correction output). I tried running the analysis with the -no-whiten flag and it made no difference. When this data is analyzed with Brain Voyager by others in my lab, this problem doesn't exist, and you see appropriate activity for the vs. fixation conditions. When I run data collected with PACE, I don't have this comparison to fixation problem, but I do for nonPACE bold runs. Commands I ran: mkanalysis-sess -analysis infIPS -TR 2 -paradigm loc.dat -designtype blocked -funcstem fmc -motioncor -runlistfile loc_runs.txt -inorm -nskip 2 -nconditions 2 -timewindow 20 -gammafit 2.25 1.25 -noautostimdur mkcontrast-sess -analysis infIPS -contrast shape_vs_fix -a 2 -c 0 mkcontrast-sess -analysis infIPS -contrast noise_vs_fix -a 1 -c 0 mkcontrast-sess -analysis infIPS -contrast shape_vs_noise -a 2 -c 1 mkcontrast-sess -analysis infIPS -contrast act_vs_fix -a 2 -a 1 -c 0 selxavg3-sess -sf loc_loc-sess -df loc_loc.dir -analysis infIPS Any thoughts? Katie On Fri, Nov 12, 2010 at 4:19 PM, Katie Bettencourt <kcrum(a)bu.edu> wrote: > This is in blocked designs and in event related gamma designs (I haven't > had time to finish sorting out my FIR problems, so that's a different > email), but they've all boiled down to essentially these sets of commands: > > mkanalysis-sess.new -analysis num_loc -TR 2 -paradigm num.dat -designtype > blocked -funcstem fmc -runlistfile num_runs.txt -inorm -nconditions 4 > -timewindow 20 -gammafit 2.25 1.25 > > mkcontrast-sess -analysis num_loc -contrast act_vs_fix -a 1 -a 2 -a 3 -a 4 > -c 0 > mkcontrast-sess -analysis num_loc -contrast lnum_vs_snum -a 1 -c 2 > ...etc... > > preproc-sess -nosmooth -sf num-sess -df num.dir > > selxavg3-sess -sf num-sess -df num.dir -analysis num_loc -skip > -or- > selxavg-sess -sf num-sess -df num.dir -analysis num_loc > > stxgrinder-sess -analysis num_loc -contrast [contrastname here] -sf > num-sess -df num.dir > > I have tried running the same (w/ selxavg3-sess) as above but with using: > 1. the -nskip 2 flag in mkanalysis-sess.new to skip the first 2 TRs (no > change) > 2. using mkanalysis-sess (no .new) with the -no-whiten flag > 3. getting rid of the -timewindow flag > 4. running stxgrinder-sess and paint-sess after selxavg3-sess to get the > sig-0-lh and sig-0-rh files > > None of these things have had any effect. I've checked the motion > parameters and they haven't moved much. The raw data seems fine because it > analyzes fine in BrainVoyager (which I don't want to use for a multitude of > reasons, but others in my lab do use). I still end up with the entire brain > activating and activating strongly for the baseline conditions, but only if > the data were acquired using nonPACE BOLD runs and only if I use > selxavg3-sess. My PACE data is fine in both. > > Katie > > > On Fri, Nov 12, 2010 at 3:29 PM, Douglas N Greve < > greve(a)nmr.mgh.harvard.edu> wrote: > >> And this is not usging FIR, right? Can you send me your mkanalysis-sess >> commands for selxavg-sess and selxavg3-sess? >> >> Katie Bettencourt wrote: >> >>> That's ok, we;ve gone back and forth a bit. >>> >>> The real problem is that when I use selxavg3-sess on data collected in >>> non PACE sequences, it looks fine in contrasts that aren't against baseline >>> (the 0 condition in the paradigm files) but when I look at conditions vs >>> baseline (like act-vs-fix) the entire brain shows strong activation for the >>> baseline condition (I had attached pictures originally, but basically >>> imaging a brain that looks pretty much all blue and you get an accurate >>> picture). When I used selxavg-sess instead, I see a little less activation >>> for the comparisons that aren't against baseline, but appropriate pictures >>> when I compare against baseline. >>> >>> As I've said, this data has been analyzed in Brain voyager and looks fine >>> (actually stronger) but doesn't work in Freesurfer right. The activity I >>> see with selxavg3-sess when I compare nonbaseline conditions (ie. >>> shape-vs-noise) appears to be in similar locations in both Freesurfer and >>> BrainVoyager (though again weaker in Freesurfer for same thresholds). It's >>> really just the comparison to baseline that seems to be screwed up. >>> >>> Katie >>> >>> On Fri, Nov 12, 2010 at 3:11 PM, Douglas N Greve < >>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >>> >>> sorry, I've lost track of what the problem is exactly. If I >>> remember: you analyze using selxavg-sess and brain voyager and >>> things look ok, but in selxavg3-sess you lose activation? >>> >>> doug >>> >>> Katie Bettencourt wrote: >>> >>> I tried it with the -no-whiten flag and again there is no >>> difference between the -no-whiten and the normal version. Any >>> other thoughts? The only thing that seems to come up is that >>> when the data is collected with a PACE sequence I don't get >>> this problem, but a standard BOLD sequence does. I would >>> assume it was motion or something, but the motion parameters >>> are small and the data works fine in brain voyager. >>> >>> The only thing I think that is done different in brain voyager >>> is that they skip the first 2 TRs (and each experiment starts >>> with fixation), I tried to do that with the -nskip 2 option, >>> do I need to also use the -tpef function or is that only if >>> your paradigm file doesn't start at 0? >>> >>> Katie >>> >>> On Fri, Nov 12, 2010 at 1:02 PM, Katie Bettencourt >>> <kcrum(a)bu.edu <mailto:kcrum@bu.edu> <mailto:kcrum@bu.edu >>> >>> <mailto:kcrum@bu.edu>>> wrote: >>> >>> No, it was with .new should I be using mkanalysis-sess usually >>> instead of mkanalysis-sess.new? What exactly is the >>> difference? >>> >>> >>> Katie >>> >>> >>> On Fri, Nov 12, 2010 at 1:00 PM, Douglas N Greve >>> <greve(a)nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>>> wrote: >>> >>> Is it in mkanalysis-sess (without the ".new")? >>> >>> Katie Bettencourt wrote: >>> >>> I tried using the no-whiten flag with >>> mkanalysis.new and >>> it said there was no such flag and I can't find any >>> reference to it on the wiki. >>> >>> Katie >>> >>> On Wed, Nov 10, 2010 at 5:31 PM, Douglas N Greve >>> <greve(a)nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: >>> >>> >>> Can you create a new analysis using the >>> -no-whiten flag >>> and re-run >>> selxavg3-sess? For the other error, you need to >>> select >>> a prestim >>> and timewindow that are integer multiples of 1.5. >>> >>> doug >>> >>> Katie Bettencourt wrote: >>> >>> So this data has been previously analyzed in >>> BrainVoyager, and >>> there is no problems with it, subject >>> movement is >>> very low (< >>> 2mm across all runs and timepoints), though >>> I did >>> notice that >>> this problem does not happen when I analyze data >>> collected >>> with PACE sequences, and not with ones that >>> do not >>> use PACE. >>> I tried running the selxavg3-sess with the >>> -svres-unwhitened >>> (which is the only whitening related command I >>> could see), but >>> it made no difference. I'm not sure how to >>> look at >>> the raw >>> data precisely, but I do know it works >>> correctly in BV. >>> >>> Any other thoughts on what's going wrong >>> here? Can >>> I at least >>> trust the data that isn't against baseline >>> in this >>> case? It >>> looks similar, though weaker to the same data >>> analyzed with >>> BrainVoyager (not sure why I keep getting weaker >>> activation in >>> Freesurfer than Brainvoyager, but that's a >>> different >>> consideration). >>> >>> >>> Somewhat relatedly, when I try to run a FIR >>> analysis with >>> selxavg3-sess (instead of selxavg-sess): >>> mkanalysis-sess.new -analysis supIPS_loc-fir -TR >>> 1.5 -paradigm >>> supIPS.dat -designtype event-related >>> -funcstem fmc >>> -motioncor >>> -runlistfile supIPSruns.txt -inorm -nskip 2 >>> -nconditions 6 >>> -tprestim 2 -timewindow 20 >>> >>> selxavg3-sess -s 101103TM -df supIPS.dir >>> -analysis >>> supIPS_loc-fir >>> >>> I get this output/error: >>> >>> selxavg3-sess logfile is >>> >>> /home/kcb/mri-space/supIPS_loc/log/selxavg3-sess-bold-supIPS_loc-fir-101110150643.log >>> >>> -------------------------------------------------------------- >>> ------------------------------------------- >>> /home/kcb/mri-space/101103TM_supIPS >>> Wed Nov 10 15:06:43 EST 2010 >>> anadir = >>> /home/kcb/mri-space/101103TM_supIPS/bold/supIPS_loc-fir >>> ------------------------------------------ >>> ------- 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 1984-2010 The >>> MathWorks, >>> Inc. >>> Version 7.10.0.499 (R2010a) >>> 64-bit >>> (glnxa64) >>> February 5, 2010 >>> >>> To get started, type one of these: helpwin, >>> helpdesk, or demo. >>> For product information, visit >>> www.mathworks.com <http://www.mathworks.com> >>> <http://www.mathworks.com> >>> <http://www.mathworks.com> >>> <http://www.mathworks.com>. >>> >>> >>> >> >> >> >> >> >> >> >>> >>> /usr/local/freesurfer4.5/fsfast/toolbox/fast_selxavg3.m >>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>> >> >> >>> >> >> >> >>> $Id: fast_selxavg3.m,v 1.55.2.8 2009/04/17 >>> 20:09:46 >>> greve Exp $ >>> outtop = /home/kcb/mri-space >>> Extension format = nii >>> UseFloat = 0 >>> INFO: acfbins is not set, setting to 10 >>> INFO: mask is not set, setting to brain >>> 1 1_vs_fix.mat >>> 2 2_vs_1.mat >>> 3 2_vs_fix.mat >>> 4 3_vs_1.mat >>> 5 3_vs_2.mat >>> 6 3_vs_fix.mat >>> 7 4_vs_1.mat >>> 8 4_vs_2.mat >>> 9 4_vs_3.mat >>> 10 4_vs_fix.mat >>> 11 643_vs_2-delay.mat >>> 12 643_vs_2.mat >>> 13 6_vs_1.mat >>> 14 6_vs_2.mat >>> 15 6_vs_3.mat >>> 16 6_vs_4.mat >>> 17 6_vs_fix.mat >>> 18 act_vs_fix.mat >>> 19 allvres.mat >>> 20 omnibus.mat >>> 21 zallvres.mat >>> 22 zomnibus.mat >>> ERROR: psdmin=-2 not int mult of dpsd=1.5 >>> ERROR: psdmax=17.5 not int mult of dpsd=1.5 >>> ??? Index exceeds matrix dimensions. >>> >>> Error in ==> fast_condctrstmtx at 102 >>> Rpost = diag(WDelays(nnpost)); % Diagonal >>> PostStim Weights >>> >>> Error in ==> flac_conmat at 64 >>> R = >>> >>> fast_condctrstmtx(dpsd,TW,-psdmin,con.sumevreg,WDelay,1); >>> >>> Error in ==> fast_ldanaflac at 474 >>> flactmp = flac_conmat(flac,nthcon); >>> >>> Error in ==> fast_selxavg3 at 85 >>> flac0 = fast_ldanaflac(analysis); >>> >> ------------------------------------------ >>> ERROR: fast_selxavg3() failed\n >>> >>> >>> Katie >>> >>> On Wed, Nov 10, 2010 at 11:03 AM, Douglas N >>> Greve >>> <greve(a)nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>>> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: >>> >>> I have no idea what is happening, but I can >>> suggest a few >>> checks. Have >>> you looked at the motion correction >>> plots? Have >>> you looked >>> at the raw >>> data? Another thing to try is to turn off >>> whitening when >>> you make the >>> analysis for selxavg3-sess. >>> >>> doug >>> >>> Katie Bettencourt wrote: >>> > Hi all, >>> > >>> > I'm still trying to figure out what's >>> going on >>> with the >>> differences >>> > I'm getting between selxavg-sess and >>> selxavg3-sess. I"m >>> using >>> > freesurfer4.5. I was using >>> selxavg3-sess (as >>> suggested on >>> the wiki) >>> > but I was getting weird activation maps >>> when I >>> compared any >>> condition >>> > vs. baseline, where most of the brain >>> was more >>> activity >>> for baseline >>> > (which was fixation) - see the attached >>> picture for >>> > act-fix-gamma-selxavg3-rh.png. So I ran >>> selxavg-sess >>> which was >>> what >>> > I used to run with an older version of >>> freesurfer, and when I >>> did this >>> > I got a more appropriate picture - see >>> act-fix-gamma-rh.png >>> > >>> > The experiment starts with fixation >>> (baseline) >>> so I tried >>> running the >>> > analysis with and without skipping the >>> first 2 >>> TRs to account >>> for the >>> > BOLD spike, but it makes no difference >>> in the >>> activation map. >>> > >>> > These are essentially the commands I ran: >>> > mkanalysis-sess.new -analysis loc_loc -TR 2 >>> -paradigm loc.dat >>> > -designtype blocked -funcstem fmc >>> -runlistfile >>> loc_runs.txt -inorm >>> > -nconditions 2 -timewindow 20 -gammafit >>> 2.25 1.25 >>> > >>> > mkcontrast-sess -analysis loc_loc -contrast >>> shape_vs_fix >>> -a 2 -c 0 >>> > >>> > selxavg3-sess -s 101006SP_loc_loc -df >>> loc_loc.dir >>> -analysis loc_loc >>> > >>> > >>> > Thoughts? Or should I just not use >>> selxavg3-sess? >>> > >>> > Katie >>> > >>> > >>> > ---------- Forwarded message ---------- >>> > From: *Katie Bettencourt* <kcrum(a)bu.edu >>> <mailto:kcrum@bu.edu> >>> <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>> >>> <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu> >>> <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>>> >>> <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu> >>> <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>> >>> <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu> >>> <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>>>> >>> <mailto:kcrum@bu.edu >>> <mailto:kcrum@bu.edu> <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>> >>> <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu> >>> <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>>> >>> <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu> >>> <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>> >>> <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu> >>> <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>>>>>> >>> > Date: Tue, Nov 2, 2010 at 2:31 PM >>> > Subject: Questions about event related >>> processing and >>> selxavg-sess and >>> > selxavg3-sess >>> > To: freesurfer maillist >>> <freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> <mailto:freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu>>> >>> <mailto:freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> <mailto:freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu>>>> >>> > <mailto:freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> <mailto:freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu>>> >>> <mailto:freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> <mailto:freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu>>>>>> >>> > >>> > >>> > Hi all, >>> > >>> > I've been trying to analyses both an event >>> related and >>> block design >>> > experiments and have noticed a couple >>> things >>> that are >>> confusing >>> me and >>> > I would appreciate any help anyone >>> could give me. >>> > >>> > 1. In trying do the event-related >>> analysis, >>> I'm am a bit >>> confused by >>> > the FIR vs Gamma analysis and the use >>> of the >>> time window and >>> tprestim >>> > in the FIR analysis. I have an experiment >>> with 6 set size >>> conditions >>> > and 1 fixation condition. each trial is 6s >>> long with a >>> TR of 1.5 >>> > >>> > I have run both of these commands: >>> > >>> > mkanalysis-sess.new -analysis >>> supIPS_loc -TR >>> 1.5 -paradigm >>> supIPS.dat >>> > -designtype event-related -funcstem fmc >>> -motioncor >>> -runlistfile >>> > supIPSruns.txt -inorm -nskip 2 >>> -nconditions 6 >>> -gammafit >>> 2.25 1.25 >>> > >>> > mkanalysis-sess.new -analysis >>> supIPS_loc -TR >>> 1.5 -paradigm >>> supIPS.dat >>> > -designtype event-related -funcstem fmc >>> -motioncor >>> -runlistfile >>> > supIPSruns.txt -inorm -nskip 2 >>> -nconditions 6 >>> -tprestim 2 >>> -timewindow 20 >>> > >>> > >>> > The FIR gives me a time course window, >>> which >>> makes me >>> think that >>> > perhaps that is the one I want to use, >>> but it >>> shows very >>> little >>> > activation. This data has been previously >>> analyzed in Brain >>> Voyager, >>> > so I know it's not a case of the conditions >>> not actually >>> causing >>> > activation, but for some reason, the FIR >>> analysis doesn't >>> show any. >>> > I'm not sure if this is due to a bad time >>> window/tprestim >>> settings, or >>> > something else. However the gamma fit >>> analysis shows a >>> bunch of >>> > activity where I expect to see it, but >>> no time >>> course window. >>> > (attached are pngs of the differences >>> for the >>> act_vs_fixation >>> > comparison). >>> > >>> > >>> > 2. In addition, in both the event related >>> (gamma) and a >>> normal >>> block >>> > design (different experiment) I get >>> very different >>> results (at least >>> > for certain comparisons) depending on >>> whether >>> I use >>> selxavg-sess >>> (with >>> > stxgrinder-sess for each contrast) or >>> selxavg3-sess. The >>> differences >>> > are shown in the attached pngs >>> (act_vs_fix-gamma.png >>> (which is the >>> > selxavg-sess and stxgrinder-sess >>> analysis and >>> > act_vs_fix-gamma-selxavg3). In the block >>> design, both >>> selxavg3 and >>> > selxavg (+stxgrinder) give me very similar >>> activation >>> when comparing >>> > two non-null conditions (ie. >>> shape_vs_noise) >>> but very >>> different (and >>> > similar to the differences in the attached >>> pictures) >>> activations >>> when >>> > comparing against the null (ie >>> shape_vs_fix or >>> noise_vs_fix). >>> What am >>> > I doing wrong here? >>> > >>> > Thanks for your help! >>> > >>> > Katie >>> > >>> > >>> > >>> >>> ------------------------------------------------------------------------ >>> > >>> > >>> > >>> >>> ------------------------------------------------------------------------ >>> > >>> > >>> >>> ------------------------------------------------------------------------ >>> > >>> > >>> _______________________________________________ >>> > Freesurfer mailing list >>> > Freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> >>> >>> > >>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>>> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>>>> >>> >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: >>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> > >>> < >>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> < >>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> >>> FileDrop: >>> >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> < >>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> < >>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> < >>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@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. >>> >>> >>> >>> -- Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>>> >>> Phone Number: 617-724-2358 Fax: 617-726-7422 >>> >>> Bugs: >>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> > >>> < >>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop: >>> >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> < >>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> < >>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> >>> >>> >>> -- Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> >>> Phone Number: 617-724-2358 Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop: >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> < >>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> >>> >>> >>> >>> -- Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> Phone Number: 617-724-2358 Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >

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Is it possible to unload patch ?
by Vadim Axel 02 Dec '10

02 Dec '10

Hi, After loading, for example, flattened patch I would like to go back to a standard, inflated brain without patch while I preserve all my overlays. Is it possible? Thanks, Vadim

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Re: [Freesurfer] Help with generation of surface after WM edits
by Douglas N Greve 01 Dec '10

01 Dec '10

You can ignore that error. Does the lh.orig.nofix look the same before and after the wm edits? doug SK wrote: > Hi, > > I ran the command > >> recon-all -autorecon2-wm -subjid George -noaseg >> > after reading your comments and it finally finished just now. But I > still cannot see any changes in the places where I have modified the > white matter. > > So, i tried loading the lh.orig.nofix using > > >> tkmedit Paul wm.mgz lh.orig.nofix >> > > It shows a zagged yellow line on top of the wm.mgz. There is also an > error saying.. > > >> mrisReadTriangleFile(/data/kodaly/r/sk/FreeSurfer/Paul/surf/lh.orig): surface >doesn't match /data/kodaly/r/sk/FreeSurfer/Paul/surf/lh.orig.nofix >> > > Any suggestions?? > > regards, > krishna > > > > On 11/30/10, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: > >> That is strange. The -autorecon2-wm should have changed those surfaces. >> What's in your xopts file? Can you load the lh.orig.nofix surface in >> tkmedit to see if that has changed? >> >> doug >> >> Krishna Srihasam wrote: >> >>> Hi, >>> >>> I am trying to generate surfaces of a monkey brain and I have run into >>> some problem after the initial surface creation. I had some problems >>> with wm.mgz and I corrected them (check the two images I have >>> attached). I then ran >>> >>> recon-all -autorecon2-wm -subjid George -noaseg –xopts-use –nocortribbon >>> >>> The pial and wm surfaces output was exactly similar to the older one >>> (i.e. before the white matter edits).I , then, tried running recon-all >>> with >>> >>> recon-all -autorecon2-pial -subjid George -noaseg –xopts-use >>> –nocortribbon >>> >>> with pretty much the same result. Any help , suggestions or input is >>> more that welcome. >>> >>> Regards, >>> >>> Krishna >>> >>> >>> ------------------------------------------------------------------------ >>> >>> >>> ------------------------------------------------------------------------ >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> >> 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. >> >> >> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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mask.mgh to volume
by Ritobrato Datta 01 Dec '10

01 Dec '10

Hello All , I have a binary mask - mask.mgh. I want create a binary volumetric mask from it in the same space and dimension as orig.mgz Can mri_label2vol be used ? How ? If not, how can this be done ? Thanks a lot Ri

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func2roi-sess question : label2mask_linear: there were 0 label hits
by Yuko Yotsumoto 01 Dec '10

01 Dec '10

Hi all, Mac OS 10.6.5 freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 I want to run func2roi-sess with a functionally defined label (lh_MT.label). I have a label stored as : subjects/VM20/label/lh_MT.label and I can see this label with tksurfer-sess. When I ran: func2roi-sess -roidef lh_MT -analysis VMfwhm5lh -motioncor -rawstem fmcsm5 -df sessdirfile -reg register.dof6.dat -s VM20 -anatlabel lh_MT I got an error (roisummary-sess results filled with 0). Below shows some lines from log file that might be related to this problem. All logs are pasted at the end of this message. > Lxyz2Scrs: > -1.000 -0.020 0.021 69283.891; > 0.019 -1.000 -0.021 -1.705; > 0.022 -0.021 1.000 -19.485; > 0.000 0.000 0.000 1.000; > > INFO: label2mask_linear: there were 0 label hits > voxsize = 1, rszthresh = 1e-07, thresh = 1e-07 > INFO: label2mask_linear: there were 0 hits in final mask > label2mask_linear: done > > Lxyz2Scrs: > -1.000 -0.020 0.021 69283.891; > 0.019 -1.000 -0.021 -1.705; > 0.022 -0.021 1.000 -19.485; > 0.000 0.000 0.000 1.000; > > INFO: label2mask_linear: there were 0 label hits > voxsize = 1, rszthresh = 1e-07, thresh = 1e-07 > INFO: label2mask_linear: there were 0 hits in final mask > label2mask_linear: done > Averging over ROI Looks like somehow my label was rejected, or didn't meet some criteria? I don't want any functional thresholds for this analysis, though I see clear activation within this label during task. Please let me know what I need to add/change to make func2roi-sess work. Thank you! Yuko Yotsumoto ############################################### fucn2roi-sess log file $Id: func2roi-sess,v 1.16 2010/03/25 16:22:53 greve Exp $ /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan /Applications/freesurfer/fsfast/bin/func2roi-sess -roidef lh_MT -analysis VMfwhm5lh -motioncor -rawstem fmcsm5 -df sessdirfile -reg register.dof6.dat -s VM20 -anatlabel lh_MT Darwin Yukos-iMac.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 Tue Nov 30 13:08:07 JST 2010 ----------------------------------------------------- Session: VM20 1/1 Tue Nov 30 13:08:07 JST 2010 Tue Nov 30 13:08:07 JST 2010 --------------------------------------------------- /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20 mri_vol2roi --srcvol bold/VMfwhm5lh/h --roiavg bold/VMfwhm5lh/lh_MT/h --srcreg bold/register.dof6.dat --label /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label --finalmskvol bold/VMfwhm5lh/lh_MT/mask --roiavgtxt bold/VMfwhm5lh/lh_MT/h.txt --------------------------------------------------- -------------------------------------------------------- /Users/yuko/Documents/freesurfer/sessions/VM/VM20 mri_vol2roi --srcvol bold/VMfwhm5lh/h --roiavg bold/VMfwhm5lh/lh_MT/h --srcreg bold/register.dof6.dat --label /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label --finalmskvol bold/VMfwhm5lh/lh_MT/mask --roiavgtxt bold/VMfwhm5lh/lh_MT/h.txt version $Id: mri_vol2roi.c,v 1.31 2010/03/25 16:00:50 greve Exp $ -------------------------------------------------------- roifile = bold/VMfwhm5lh/lh_MT/h roitxtfile = bold/VMfwhm5lh/lh_MT/h.txt oldtxtstyle = 0 srcvol = bold/VMfwhm5lh/h.nii srcfmt = bvolume srcreg = bold/register.dof6.dat srcregold = 0 srcwarp unspecified label file = /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label labelreg unspecified label fill thresh = 1e-07 mskvol unspecified Loading volume bold/VMfwhm5lh/h.nii ...done srcreg Dsrc ------------- 1.000 0.020 -0.021 -0.890; 0.022 -0.021 1.000 -19.985; -0.019 1.000 0.021 2.205; 0.000 0.000 0.000 1.000; ---------------------------------- ras2vox src (tkreg) Qsrc ------------- -1.000 0.000 0.000 69283.000; -0.000 -0.000 -1.000 0.500; -0.000 1.000 -0.000 0.500; 0.000 0.000 0.000 1.000; ---------------------------------- INFO: Source volume detected as selxavg format INFO: Adjusting Frame Power Lxyz2Scrs: -1.000 -0.020 0.021 69283.891; 0.019 -1.000 -0.021 -1.705; 0.022 -0.021 1.000 -19.485; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 0 label hits voxsize = 1, rszthresh = 1e-07, thresh = 1e-07 INFO: label2mask_linear: there were 0 hits in final mask label2mask_linear: done Lxyz2Scrs: -1.000 -0.020 0.021 69283.891; 0.019 -1.000 -0.021 -1.705; 0.022 -0.021 1.000 -19.485; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 0 label hits voxsize = 1, rszthresh = 1e-07, thresh = 1e-07 INFO: label2mask_linear: there were 0 hits in final mask label2mask_linear: done Averging over ROI INFO: vol2maskavg: nhits = 0 WARNING: there were no voxels in the input mask > 0.5 Done averging over ROI (nhits = 0) INFO: Readjusting Frame Power --------------------------------------------------- /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20 mri_vol2roi --srcvol bold/VMfwhm5lh/h-offset --roiavg bold/VMfwhm5lh/lh_MT/h-offset --srcreg bold/register.dof6.dat --label /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label --finalmskvol bold/VMfwhm5lh/lh_MT/mask --roiavgtxt bold/VMfwhm5lh/lh_MT/h-offset.txt --------------------------------------------------- -------------------------------------------------------- /Users/yuko/Documents/freesurfer/sessions/VM/VM20 mri_vol2roi --srcvol bold/VMfwhm5lh/h-offset --roiavg bold/VMfwhm5lh/lh_MT/h-offset --srcreg bold/register.dof6.dat --label /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label --finalmskvol bold/VMfwhm5lh/lh_MT/mask --roiavgtxt bold/VMfwhm5lh/lh_MT/h-offset.txt version $Id: mri_vol2roi.c,v 1.31 2010/03/25 16:00:50 greve Exp $ -------------------------------------------------------- roifile = bold/VMfwhm5lh/lh_MT/h-offset roitxtfile = bold/VMfwhm5lh/lh_MT/h-offset.txt oldtxtstyle = 0 srcvol = bold/VMfwhm5lh/h-offset.nii srcfmt = bvolume srcreg = bold/register.dof6.dat srcregold = 0 srcwarp unspecified label file = /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label labelreg unspecified label fill thresh = 1e-07 mskvol unspecified Loading volume bold/VMfwhm5lh/h-offset.nii ...done srcreg Dsrc ------------- 1.000 0.020 -0.021 -0.890; 0.022 -0.021 1.000 -19.985; -0.019 1.000 0.021 2.205; 0.000 0.000 0.000 1.000; ---------------------------------- ras2vox src (tkreg) Qsrc ------------- -1.000 0.000 0.000 69283.000; -0.000 -0.000 -1.000 0.500; -0.000 1.000 -0.000 0.500; 0.000 0.000 0.000 1.000; ---------------------------------- Lxyz2Scrs: -1.000 -0.020 0.021 69283.891; 0.019 -1.000 -0.021 -1.705; 0.022 -0.021 1.000 -19.485; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 0 label hits voxsize = 1, rszthresh = 1e-07, thresh = 1e-07 INFO: label2mask_linear: there were 0 hits in final mask label2mask_linear: done Lxyz2Scrs: -1.000 -0.020 0.021 69283.891; 0.019 -1.000 -0.021 -1.705; 0.022 -0.021 1.000 -19.485; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 0 label hits voxsize = 1, rszthresh = 1e-07, thresh = 1e-07 INFO: label2mask_linear: there were 0 hits in final mask label2mask_linear: done Averging over ROI INFO: vol2maskavg: nhits = 0 WARNING: there were no voxels in the input mask > 0.5 Done averging over ROI (nhits = 0) ------------------------------------------- /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20 mri_vol2roi --srcvol bold/001/ --roiavg bold/VMfwhm5lh/lh_MT/-001 --srcreg bold/register.dof6.dat --label /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label --finalmskvol bold/VMfwhm5lh/lh_MT/mask --roiavgtxt bold/VMfwhm5lh/lh_MT/-001.txt ------------------------------------------- corRead(): can't open file bold/001/COR-.info -------------------------------------------------------- /Users/yuko/Documents/freesurfer/sessions/VM/VM20 mri_vol2roi --srcvol bold/001/ --roiavg bold/VMfwhm5lh/lh_MT/-001 --srcreg bold/register.dof6.dat --label /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label --finalmskvol bold/VMfwhm5lh/lh_MT/mask --roiavgtxt bold/VMfwhm5lh/lh_MT/-001.txt version $Id: mri_vol2roi.c,v 1.31 2010/03/25 16:00:50 greve Exp $ -------------------------------------------------------- roifile = bold/VMfwhm5lh/lh_MT/-001 roitxtfile = bold/VMfwhm5lh/lh_MT/-001.txt oldtxtstyle = 0 srcvol = bold/001/ srcfmt = bvolume srcreg = bold/register.dof6.dat srcregold = 0 srcwarp unspecified label file = /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label labelreg unspecified label fill thresh = 1e-07 mskvol unspecified Loading volume bold/001/ ...

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occipital label without v1
by Ritobrato Datta 01 Dec '10

01 Dec '10

Hello All, I have an occipital label and a v1 label and I have created binary masks from them. Is there a way to create an "Occipital label - V1 label" ie excluding v1 from occipital label. Please let me know. Thank you Ri

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some pial-like tissues aroud Coronal 117 slices
by xuemei lei 01 Dec '10

01 Dec '10

Hi, experts I found my data with a problem like the attached picture: around Coronal 117 slice there are some pial-like tissue included in gray matter。I am not sure this kind of things are pials or gray matter and if I should remove them from the GM. Any help will be appreciated. Thanks in advance -- Xuemei Lei National Key Laboratory of Cognitive Neuroscience and Learning<http://psychbrain.bnu.edu.cn> Beijing Normal University Beijing, China. 100875 Tel: +86-13269171259 ============================================== Welcome to visit my blog: www.mobiye.com

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Freesurfer December 2010