Freesurfer November 2010

freesurfer@nmr.mgh.harvard.edu

92 participants
127 discussions

selxavg-sess vs selxavg3-sess
by Katie Bettencourt 10 Nov '10

10 Nov '10

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> 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> 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

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Problem with mri_segstats
by Elizabeth Gutierrez 10 Nov '10

10 Nov '10

Hi, I've been trying to use mri_segstats on a FA map with a white matter parcellation file (wmparc.mgz) but there might be a problem in the program. When I open the fa.stats output file, all the values (std.dev, etc) are 0.0000 for the 2009 table parcellation ids. However, when I use the label id 251 (corpus collosum) from the first few labels on the list, I get a value. When I use the corpus collosum id for more current labels like the aparc 2005 and 2009, I get 0.0000 again. Could there be a bug in the program? -- Elizabeth C. Gutierrez Graduate Student Department of Brain and Cognitive Sciences Massachusetts Institute of Technology

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Re: [Freesurfer] -noconform flag of mri_normalize doesn't work
by "Falk Lüsebrink" 10 Nov '10

10 Nov '10

Hi Bruce, I'm so sorry, I should have double-checked. You are completely right; mri_normalize does work perfectly fine. The conformation to 1mm isotropic is done in the last step of mri_nu_correct.mni. In the last step of mri_nu_correct.mni the --conform flag is used, which shouldn't be used: ************************************ mri_convert ./tmp.mri_nu_correct.mni.32343/nu1.mnc nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.32343/nu1.mnc nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from ./tmp.mri_nu_correct.mni.32343/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 2.12874e-08) j_ras = (3.72529e-08, 0, -1) k_ras = (0, 1, 0) Original Data has (0.7, 0.7, 0.7) mm size and (321, 321, 321) voxels. Data is conformed to 1 mm size and 256 voxels for all directions INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to nu.mgz... Wed Nov 10 10:47:32 CET 2010 mri_nu_correct.mni done ************************************ Also attached is the recon-all.log and the output of mri_info of orig.mgz and nu.mgz. Thanks again, Falk Lüsebrink -------- Original-Nachricht -------- > Datum: Tue, 9 Nov 2010 21:06:49 -0500 (EST) > Von: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > An: "Falk Lüsebrink" <falk.luese(a)gmx.net> > CC: freesurfer(a)nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] -noconform flag of mri_normalize doesn\'t work > Hi Falk, > > I just tried it and it seemed to work for me: > > mri_info Gaab20070225a/mri/rawavg.mgz > Volume information for Gaab20070225a/mri/rawavg.mgz > type: MGH > dimensions: 256 x 256 x 128 > voxel sizes: 1.0000, 1.0000, 1.3300 > type: SHORT (4) > fov: 256.000 > dof: 0 > xstart: -128.0, xend: 128.0 > ystart: -128.0, yend: 128.0 > zstart: -85.1, zend: 85.1 > TR: 2000.00 msec, TE: 3.44 msec, TI: 900.00 msec, flip angle: > 9.00 degrees > nframes: 1 > PhEncDir: ROW > ras xform present > xform info: x_r = 0.5924, y_r = 0.0086, z_r = -0.8056, c_r = > -9.9942 > : x_a = -0.7780, y_a = -0.2537, z_a = -0.5747, c_a = > 13.5548 > : x_s = 0.2093, y_s = -0.9672, z_s = 0.1436, c_s = > -22.2562 > > mri_normalize -noconform rawavg.mgz test.mgz > not interpolating and embedding volume to be 256^3... > reading from rawavg.mgz... > normalizing image... > MRInormInit: > Talairach origin at (142, 110, 71) > wsize 10, windows 14 above, 9 below > max gradient 1.000 > . > . > . > mri_info test.mgz > Volume information for test.mgz > type: MGH > dimensions: 256 x 256 x 128 > voxel sizes: 1.0000, 1.0000, 1.3300 > type: SHORT (4) > fov: 256.000 > dof: 0 > xstart: -128.0, xend: 128.0 > ystart: -128.0, yend: 128.0 > zstart: -85.1, zend: 85.1 > TR: 2000.00 msec, TE: 3.44 msec, TI: 900.00 msec, flip angle: > 9.00 degrees > nframes: 1 > PhEncDir: UNKNOWN > ras xform present > xform info: x_r = 0.5924, y_r = 0.0086, z_r = -0.8056, c_r = > -9.9942 > : x_a = -0.7780, y_a = -0.2537, z_a = -0.5747, c_a = > 13.5548 > : x_s = 0.2093, y_s = -0.9672, z_s = 0.1436, c_s = > -22.2562 > > > > On Tue, 9 Nov 2010, Falk > Lüsebrink wrote: > > > Dear FreeSurfers, > > > > The -noconform flag of mri_normalize doesn't seem to work properly in > the centos4_x86_64_stable-pub-v5.0.0 build. I have been trying to process a > volume with a native isotropic resolution of 0.7mm using recon-ll including > the -cm flag to conform the input to minimum. But during the normalization > of mri_normalize the volume is conformed to an isotropic resolution of 1mm. > > > > The flag is correctly used during mri_normalize, but it doesn't seem to > do anything. The recon-all log says: > > > > "not interpolating and embedding volume to be 256^3..." > > > > But the output volume T1.mgz is conformed to 256^3 and therefore to an > isotropic resolution of 1mm. This also happens if mri_normalize is used by > hand using the -noconform flag. > > > > A fix is highly appreciated. > > > > Thanks in advance, > > Falk Lüsebrink > > > > > > -- GRATIS! Movie-FLAT mit über 300 Videos. Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome

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-noconform flag of mri_normalize doesn't work
by Falk Lüsebrink 09 Nov '10

09 Nov '10

Dear FreeSurfers, The -noconform flag of mri_normalize doesn't seem to work properly in the centos4_x86_64_stable-pub-v5.0.0 build. I have been trying to process a volume with a native isotropic resolution of 0.7mm using recon-ll including the -cm flag to conform the input to minimum. But during the normalization of mri_normalize the volume is conformed to an isotropic resolution of 1mm. The flag is correctly used during mri_normalize, but it doesn't seem to do anything. The recon-all log says: "not interpolating and embedding volume to be 256^3..." But the output volume T1.mgz is conformed to 256^3 and therefore to an isotropic resolution of 1mm. This also happens if mri_normalize is used by hand using the -noconform flag. A fix is highly appreciated. Thanks in advance, Falk Lüsebrink

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qdec with custom paths?
by Mishkin Derakhshan 09 Nov '10

09 Nov '10

Hi, My data is not in the usual SUBJECTS_DIR/fsid structure. 1. Is it possible to run qdec so that it loads each subject from a full path instead of expecting them all to be under the same SUBJECTS_DIR? ie. with something like this: qdec.table.dat path_to_fsid gender age /full/path/fsid1 Male 23 /full/otherpath/fsid2 Female 27 2. If not, do you think creating a new common subjects dir and then using symbolic links will work? 3. If not, would I have to copy the entirety of the <fsid> directory, or do I only need a select few subdirs like the surf/ and stats/ ? thanks, mishkin

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posible error in BrainSegVol (aseg.stats) ?...
by Gonzalo Rojas Costa 09 Nov '10

09 Nov '10

Hi: There could be an error in the computation of BrainSegVol (aseg.stats) ?... How can I check it ?... Sincerely, Gonzalo Rojas Costa

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A question about VirtualBox version of FreeSurfer Ver 5.0
by Guang Zeng 09 Nov '10

09 Nov '10

Hi, there, I tried to use the VirtualBox version of FreeSurfer Ver 5.0 (I downloaded freesurfer-Virtualbox-linux-x86-stable-pub-v5.0.0-full.vdi) My system is Windows 7 64-bits, the VirtualBox I am using is Version 3.2.10 r66523, I tried to select Ubuntu and Ubuntu 64-bits as the guest OS, but after I added freesurfer-Virtualbox-linux-x86-stable-pub-v5.0.0-full.vdi, and ran it, a black window poped up, and says: "GRUB Loading stage1.5.. GRUB loading, please wait...." Then it stayed there for almost an hour, and nothing happen, Anyone can help me fix this problem? Thanks alot! Guang

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Re: [Freesurfer] Select surface vertices
by Bruce Fischl 09 Nov '10

09 Nov '10

Hi Alexander this is probably best done by running tksurfer and tkmedit simultaneously. You can save point in tkmedit and goto point in tksurfer to find the vertex. Or you can do it in freeview, which will display the vertex directly (or you can use tkmedit->tools->find nearest vertex) cheers Bruce On Tue, 9 Nov 2010, Alexander Hunold wrote: > Hello all, > > > > I segmented a brain with FreeSurfer and I am very satisfied about the > result. > After that I visualized the T1.mgz together with the white surface in > TkMedit. > Now I am looking for interesting anatomical structures. My goal is to assign > vertices in the white surface at the corresponding points and save the > coordinates or better the index of the vertices. > Later I will use the selected vertices in Matlab. I already read the surface > with <freesurfer_read_surf.m>. > > Do you have a good procedure to do that? > I appreciate any hint. > > Thank you so much in advance. > > > > Sincerely, > > Alexander > > > >

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Select surface vertices
by Alexander Hunold 09 Nov '10

09 Nov '10

Hello all, I segmented a brain with FreeSurfer and I am very satisfied about the result. After that I visualized the T1.mgz together with the white surface in TkMedit. Now I am looking for interesting anatomical structures. My goal is to assign vertices in the white surface at the corresponding points and save the coordinates or better the index of the vertices. Later I will use the selected vertices in Matlab. I already read the surface with <freesurfer_read_surf.m>. Do you have a good procedure to do that? I appreciate any hint. Thank you so much in advance. Sincerely, Alexander

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selxavg3-sess in OSX
by Jason Webster 09 Nov '10

09 Nov '10

I'm trying to run a retinotopic analysis with the following commands: mkanalysis-sess -analysis retino-lh -TR 2 -retinotopy 40 -paradigm rtopy.para -funcstem fmcpr.sm5.self -surface self lh -mcextreg -runlistfile retRuns -fwhm 0 selxavg3-sess -analysis retino-lh -s somesubject -df sessdir and am getting the error: >> >> >> >> >> >> >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.88.2.2 2010/07/16 15:31:24 greve Exp $ outtop = /Users/jwebst/UW/Psych/VisCog/techAdmin/anatV1LGN/pilotData/RET/data Extension format = nii ERROR: cannot determine format of /Users/jwebst/UW/Psych/VisCog/techAdmin/anatV1LGN/pilotData/RET/data/nsLGHa/bold/001/fmcpr.sm5.self ERROR: attempting to read /Users/jwebst/UW/Psych/VisCog/techAdmin/anatV1LGN/pilotData/RET/data/nsLGHa/bold/001/fmcpr.sm5.self ------------------------------------------ ERROR: fast_selxavg3() failed\n It looks like this might have something to do with analysis.info ... funcstem fmcpr.sm5.self ... RawSpace surface self lh ... Should the funcstem have gotten '.lh' or should this be worked out by getana or selxavg3-sess? Thanks, ~Jason

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Freesurfer November 2010