OK, this is a bug in 4.5 in which it ignores the nskip option. This is fixed in version 5.0. If you need to continue with 4.5, you can use a tpexclude file to remove the 1st two time points, something like:
echo "0 2" > 100524AK_infIPS/bold/007/tpexclude.dat echo "0 2" > 100524AK_infIPS/bold/014//tpexclude.dat mkanalysis-sess -analysis infIPS.new -TR 2 -paradigm loc.dat -designtype blocked -funcstem fmc -motioncor -inorm -nconditions 2 -timewindow 20 -gammafit 2.25 1.25 -noautostimdur -tpexclude tpexclude.dat I have verified that this works with your data. doug Katie Bettencourt wrote: > 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 <kc...@bu.edu > <mailto:kc...@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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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 > <kc...@bu.edu <mailto:kc...@bu.edu> > <mailto:kc...@bu.edu <mailto:kc...@bu.edu>> > <mailto:kc...@bu.edu <mailto:kc...@bu.edu> > > <mailto:kc...@bu.edu <mailto:kc...@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 > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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 > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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> > <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 > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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* > <kc...@bu.edu <mailto:kc...@bu.edu> > <mailto:kc...@bu.edu <mailto:kc...@bu.edu>> > <mailto:kc...@bu.edu > <mailto:kc...@bu.edu> <mailto:kc...@bu.edu > <mailto:kc...@bu.edu>>> > <mailto:kc...@bu.edu > <mailto:kc...@bu.edu> <mailto:kc...@bu.edu > <mailto:kc...@bu.edu>> > <mailto:kc...@bu.edu <mailto:kc...@bu.edu> > <mailto:kc...@bu.edu <mailto:kc...@bu.edu>>>> > <mailto:kc...@bu.edu > <mailto:kc...@bu.edu> <mailto:kc...@bu.edu > <mailto:kc...@bu.edu>> > <mailto:kc...@bu.edu <mailto:kc...@bu.edu> > <mailto:kc...@bu.edu <mailto:kc...@bu.edu>>> > <mailto:kc...@bu.edu > <mailto:kc...@bu.edu> <mailto:kc...@bu.edu > <mailto:kc...@bu.edu>> > <mailto:kc...@bu.edu <mailto:kc...@bu.edu> > <mailto:kc...@bu.edu <mailto:kc...@bu.edu>>>>> > <mailto:kc...@bu.edu > <mailto:kc...@bu.edu> > <mailto:kc...@bu.edu <mailto:kc...@bu.edu>> > <mailto:kc...@bu.edu <mailto:kc...@bu.edu> > <mailto:kc...@bu.edu <mailto:kc...@bu.edu>>> > <mailto:kc...@bu.edu > <mailto:kc...@bu.edu> <mailto:kc...@bu.edu > <mailto:kc...@bu.edu>> > <mailto:kc...@bu.edu <mailto:kc...@bu.edu> > <mailto:kc...@bu.edu <mailto:kc...@bu.edu>>>> > <mailto:kc...@bu.edu > <mailto:kc...@bu.edu> <mailto:kc...@bu.edu > <mailto:kc...@bu.edu>> > <mailto:kc...@bu.edu <mailto:kc...@bu.edu> > <mailto:kc...@bu.edu <mailto:kc...@bu.edu>>> > <mailto:kc...@bu.edu > <mailto:kc...@bu.edu> <mailto:kc...@bu.edu > <mailto:kc...@bu.edu>> > <mailto:kc...@bu.edu <mailto:kc...@bu.edu> > <mailto:kc...@bu.edu <mailto:kc...@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@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>>>>> > > > <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 > <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@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>>>>> > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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> > > <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> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > _______________________________________________ > Freesurfer mailing list > 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 > <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 > gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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> > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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 > gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@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 gr...@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
