Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Using mri_segstats
by Tyler Blazey 06 Dec '10

06 Dec '10

Hi, I have two questions about using mri_segstats. First, I notice that on the individual dti tutorial, you don't use the --pvol option to correct for partial voluming. Is there a reason for this? Second, would there be any disadvantage to using mri_segstats with aparc+aseg.mgz to get volume/ thickness measurements? I know from the ReconAllDevTable that the standard method is to use mris_anatomical_stats, but I need to get the stats after transforming the aparc+aseg image, so that is not an option. Thanks for any help. - Tyler

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To use the file thickness.mgh outside Freesurfer
by qizhu wu 06 Dec '10

06 Dec '10

Dear experts, I am greenhand for using FS, and am looking for ways to use the FS generated parameteric files, such as *thickness.mgh, *sulc.mgh, etc, outside FS. I got the following questions: 1. Whether these files contain coordinate information for each vertex, so I can transform them into image style file? If they do, that'll be very helpful. 2. If these files could not be tranformed into images, I am going to tranform them into ascii files using FS commands. The questions is: what's the orgnization of the output ascii file? i.e., from where to where inside the file is the header information, and does each line in the file stand for the value of a single vertex? How can I make such a ascii file which contains only vertex values in the right order? 3. I have obtained ascii files of individual's cortical thickness using mri_convert (with header inside), however, when I open it using different tools, the values look different, why? Best wishes Qizhu Wu HUaxi MR research center West China Hospital, Sichuan University

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fsaverage triangle mesh data
by Ørjan Bergmann 06 Dec '10

06 Dec '10

Dear all I am interested doing some visualization of my cortical FreeSurfer results in other software. In order to do so I need to some information about how the cortical surface is defined. Usually these surfaces consists of a set of 3D coordinates which gives the position of the vertices (163842 in the case of fsaverage), and a set of triangle definitions which are 3 indices into the vertex data (see http://en.wikipedia.org/wiki/Triangle_mesh ) Is it possible for me to access the triangle and vertex information of the cortical surface of the fsaverage subject? --- Sincerely Ørjan Bergmann, PhD Post. Doc. University of Oslo

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Create a surface from fMRI data
by Leonardo Barbosa 05 Dec '10

05 Dec '10

Hello, I've been looking through the tutorials and this list but couldn't find the answer: is it possible to create a surface from fMRI data *without* the anatomical MRI data? I know I can use mri_vol2surf but it needs a "subject" parameter, so I need to run recon-all before to create the surfaces, right? Is it possible to create a subject and surfaces (spherical, etc) with only the fMRI data? Thanks in advance for any help! Leonardo Barbosa Insituto de Física da Universidade de São Paulo if.usp.br

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funcroi-table-sess
by Yuko Yotsumoto 05 Dec '10

05 Dec '10

Hi All, I'm using : freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 I'd like to plot HDR for each condition for each subject. With FreeSurfer v4.5.0, I did so with func2roi-sess and roisummary-sess. With v5.0, those commands do not seem to work. I could get a table with: > funcroi-config -analysis VMfwhm5lh -label lh_DLPFC -roi lh.DLPFC.roicfg -contrast all_null -sign abs -thresh 1 -force > funcroi-sess -roi lh.DLPFC.roicfg -df sessdirfile -s VM20 > funcroi-table-sess -o /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan/ROIs/lh_DLPFC/lh_DLPFC_VM20.txt -roi lh.DLPFC.roicfg -df sessdirfile -s VM20 -a VMfwhm5lh -c all_null However, what I want is BOLD values in each time point for all conditions. funcroi-table-sess fails if I do not specify a contrast. > funcroi-config -analysis VMfwhm5lh -label lh_DLPFC -roi lh.DLPFC.roicfg -force > funcroi-sess -roi lh.DLPFC.roicfg -df sessdirfile -s VM20 > funcroi-table-sess -o /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan/ROIs/lh_DLPFC/lh_DLPFC_VM20.txt -roi lh.DLPFC.roicfg -df sessdirfile -s VM20 -a VMfwhm5lh ERROR: must specify a contrast Is there a command that gives me values, not a table? Thank you, Yuko

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control points-- Any tips?
by Deniz Ozgen 03 Dec '10

03 Dec '10

Hello, I have about 10 subjects that I am trying to obtain cortical segmentations. In some of the cases parts of the temporal lobes are not included in the segmentation due to low intensity (or RF bias). I tried adding control points as described in the tutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints) The wm/pial boundaries are worse than before, excluding even more parts of wm, even where I placed the control points. I added about 30-50 controls points mostly in low intensity wm strands that are not correctly segmented. I was hoping someone may have some tips or hints on good placement of control points, besides the ones on the tutorial. Trial and error is suggested in the tutorial but considering the time it takes to re-run each subject, it is too time consuming. Thanks in advance. Deniz Ozgen.

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Saving individual slices within a nifti file
by Lisa F. Akiyama 02 Dec '10

02 Dec '10

Hello, Is there a way to individually save slices within a nifti file in the nifti format using the mri_convert command? Thank you. Best, Lisa ______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington E-mail: lrisa87(a)uw.edu P Please consider the environment before printing this e-mail.

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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 >> >> >

2 1

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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