Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] Inter-hemispheric registration issue
by Douglas N Greve 04 Jun '12

04 Jun '12

Irene, this is a problem with the script. The work-around is to run xhemireg before running surfreg with the --xhemi option. doug On 05/16/2012 01:56 AM, Irene Altarelli wrote: > Dear Doug, > > here is what I get. > > First, I ran surfreg --s aa_tris --t fsaverage_sym --lh and got the > attached log file. Here is the terminal output: > > setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/ > cd /home/ialtarelli > /home/ialtarelli/freesurfer/bin/surfreg --s aa_tris --t fsaverage_sym > --lh > > Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 > x86_64 GNU/Linux > #@# lh mardi 15 mai 2012, 19:23:56 (UTC+0200) > #CMD# mris_register -curv -annot > aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg > using smoothwm curvature for final alignment > zeroing medial wall in aparc.annot > $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ > $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ > reading surface > from /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere... > reading colortable from annotation file... > colortable with 36 entries read > (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > reading template parameterization > from /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif... > ripping medial wall... > writing registered surface > to /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg... > curvature mean = 0.007, std = 0.603 > curvature mean = 0.030, std = 0.806 > curvature mean = 0.024, std = 0.853 > curvature mean = 0.009, std = 0.826 > curvature mean = 0.011, std = 0.936 > curvature mean = 0.003, std = 0.836 > curvature mean = 0.005, std = 0.972 > curvature mean = 0.001, std = 0.837 > curvature mean = 0.001, std = 0.988 > curvature mean = -0.032, std = 0.312 > curvature mean = 0.032, std = 0.124 > curvature mean = 0.079, std = 0.315 > curvature mean = 0.031, std = 0.151 > curvature mean = 0.049, std = 0.489 > curvature mean = 0.031, std = 0.165 > curvature mean = 0.028, std = 0.631 > curvature mean = 0.031, std = 0.171 > curvature mean = 0.011, std = 0.749 > 159: 0 negative triangles > surfreg-Run-Time-Hours aa_tris lh 0 0,90 > mardi 15 mai 2012, 20:17:58 (UTC+0200) > surfreg done > > Then, I ran surfreg --s aa_tris --t fsaverage_sym --lh --xhemi and the > terminal output is just: > > ERROR: cannot > find /home/ialtarelli/DATABASE/Karla5//aa_tris/xhemi/surf/lh.sphere > > without any log file, at least I can't find any modified file in the > subject's folder. > > > Hope this helps make things clearer. > Many thanks in advance! > Irene > > > Le mardi 15 mai 2012 à 15:19 -0400, Douglas N Greve a écrit : >> Can you send me the command line and terminal output? Did you run >> xhemireg first? Should not have had to ... >> >> On 05/15/2012 03:02 PM, Irene.Altarelli(a)ens.fr wrote: >>> Dear Doug, >>> >>> where would that log file be? As the /subject/xhemi fails to be created the log >>> normally appearing in there cannot be found.. Sorry if I misunderstood >>> something. >>> >>> Thanks, >>> Irene >>> >>> >>> Selon Douglas N Greve<greve(a)nmr.mgh.harvard.edu>: >>> >>>> Hi Irene, can you send the log file for the command that is failing? >>>> doug >>>> >>>> On 05/15/2012 01:28 PM, Irene Altarelli wrote: >>>>> Dear all, >>>>> >>>>> I'm trying to use the new script for the inter-hemisphere analysis, in >>>>> Fs version 5.0. I have downloaded the files as suggested >>>>> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html) >>>>> >>>>> Surfreg seems to be running fine (surfreg --s subject --t fsaverage_sym >>>>> --lh), but I have problems then with the --xhemi option. Some files >>>>> appear to be missing, I get the following error messages: >>>>> >>>>> ERROR: cannot find /path/subject/xhemi/surf/lh.sphere >>>>> ERROR: cannot find /path/subject/xhemi/surf/lh.smoothwm >>>>> ERROR: cannot find /path/subject/xhemi/surf/lh.sphere >>>>> ERROR: cannot find /path/subject/xhemi/label/lh.aparc.annot >>>>> >>>>> lh.fsaverage_sym.sphere.reg is created in $subject as it should (please >>>>> find the surfreg log below). >>>>> >>>>> Thank you in advance, >>>>> Irene >>>>> >>>>> >>>>> Log file for surfreg >>>>> samedi 12 mai 2012, 17:36:31 (UTC+0200) >>>>> >>>>> setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/ >>>>> cd /home/ialtarelli >>>>> /home/ialtarelli/freesurfer/bin/surfreg --s aa_copie --t fsaverage_sym >>>>> --lh >>>>> >>>>> Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 >>>>> x86_64 GNU/Linux >>>>> #@# lh samedi 12 mai 2012, 17:36:31 (UTC+0200) >>>>> #CMD# mris_register -curv -annot >>>>> aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.sphere >>>> /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif >>>> /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.fsaverage_sym.sphere.reg >>>>> using smoothwm curvature for final alignment >>>>> zeroing medial wall in aparc.annot >>>>> $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ >>>>> $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ >>>>> reading surface >>>>> from /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.sphere... >>>>> reading colortable from annotation file... >>>>> colortable with 36 entries read >>>>> (originally >>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>> reading template parameterization >>>>> from /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif... >>>>> ripping medial wall... >>>>> writing registered surface >>>>> to >>>> /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.fsaverage_sym.sphere.reg... >>>>> curvature mean = 0.007, std = 0.603 >>>>> curvature mean = 0.030, std = 0.806 >>>>> curvature mean = 0.024, std = 0.853 >>>>> curvature mean = 0.009, std = 0.826 >>>>> curvature mean = 0.011, std = 0.936 >>>>> curvature mean = 0.003, std = 0.836 >>>>> curvature mean = 0.005, std = 0.972 >>>>> curvature mean = 0.001, std = 0.837 >>>>> curvature mean = 0.001, std = 0.988 >>>>> curvature mean = -0.032, std = 0.312 >>>>> curvature mean = 0.032, std = 0.124 >>>>> curvature mean = 0.079, std = 0.315 >>>>> curvature mean = 0.031, std = 0.151 >>>>> curvature mean = 0.049, std = 0.489 >>>>> curvature mean = 0.031, std = 0.165 >>>>> curvature mean = 0.028, std = 0.631 >>>>> curvature mean = 0.031, std = 0.171 >>>>> curvature mean = 0.011, std = 0.749 >>>>> 159: 0 negative triangles >>>>> surfreg-Run-Time-Hours aa_copie lh 0 0,84 >>>>> samedi 12 mai 2012, 18:26:49 (UTC+0200) >>>>> surfreg done >>>>> >>>>> >>>> -- >>>> 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 >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)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 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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freeview RAS
by Oya, Hiroyuki (UI Health Care) 04 Jun '12

04 Jun '12

Dear Sir, When I view a brain volume (e.x., orig.mgz) with freeview and tkmedit, RAS coordinate differs. Why? Thank you. Hiroyuki ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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Re: [Freesurfer] tkregister question
by Shay Ohayon 04 Jun '12

04 Jun '12

Dear Doug, Following up on tkregister (lets see if my logic make sense). So, if I use --regheader, the actual transformation that will be written to register.dat will be this one ? T* = Tk_vox2ras(B) * inv(vox2rasB) * T * vox2rasA * inv(tkvox2rasA) where T maps X,Y,Z of volume A (in mm) to X,Y,Z of volume B (in mm) when mm space was obtained using vox2ras. This way, things will be compatible when I call tkregister again without the regheader? What bothered me was that if you use vox2ras to map things you get transformation T, which is actually different than the transformation you would get if you use tkvox2ras (i.e., T*). If this is the case, then I think I finally understand whats going on :) -- Shay Date: Fri, 01 Jun 2012 12:03:13 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] tkregister question To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <4FC8E7C1.6060806(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed When you use --regheader, then it uses the vox2ras transform in the header. If you pass it a register.dat file as input, then vox2ras is ignored. doug On 05/31/2012 06:39 PM, Shay Ohayon wrote: > Hi, > > Bump? > > Can someone please explain to me the puzzle described below regarding > tkregister2 and vox2ras0 (which I thought should be ignored for > registration purposes?) > > Thanks! > > -- Shay > > > On Sat, May 26, 2012 at 2:23 PM, Shay Ohayon <shay.ohayon(a)gmail.com > <mailto:shay.ohayon@gmail.com>> wrote: > > Hi, > > Here's a question to Doug / anyone else who mastered the intricate > way of volume transformations: > > I'm a bit puzzled. > According to Free surfer's documentation (fscoordinates.pdf), the > way two volumes are registered to each other using tkregister is > always using > the fixed transformation (tkvox2ras) (see page 6). > > However, when I do the following little experiment (using matlab's > freesurfer API) > > A = '001.nii'; > B = '002.nii'; > X=MRIread(A); > X.vox2ras0(1,4) = 40; > MRIwrite(X,B); > > tkregister2 --targ 001.nii --mov 002.nii --regheader -reg R.reg > > The two volumes are not in alignment when they are loaded into > tkregister. > Now, what am I missing here? > If both were loaded using the fixed transform, they should still > be in alignment (i.e., vox2ras should be ignored for registration > purposes). > > Thanks in advance, > > -- Shay > Tsao lab > Caltech > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Concatenating Transforms
by Clark Fisher 04 Jun '12

04 Jun '12

Hi everyone, What is the best way to concatenate transforms (register.dat files, .lta files, etc.)? I'm interested in registering functional data to a structural in another session using a functional to in-session anatomical registration combined with a in-session anatomical to out-of-session anatomical registration. Thanks, Clark

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Re: [Freesurfer] read_label.m produces spotty label (as compared to tksurfer)
by David Groppe 04 Jun '12

04 Jun '12

I. I use read_surf.m to import the pial surface into MATLAB: [cort.vert cort.tri]=read_surf('SUB1/surf/lh.pial'); 2. I make a completely grey color map for the surface: map=repmat([1 1 1]*.7,length(cort.vert),1); 3. I load the label into MATLAB: inlabel=read_label('SUB1','res_FINAL'); 4. I change the color map values of the vertices in the label to red: map(inlabel(:,1),:)=inlabel([1 0 0],size(inlabel,1),1); 5. I plot the surface using tripatch.m tripatch(cort,1,map); You can download a MATLAB figure that shows all the vertices of the surface color coded by label (red=label, black=non-label) from here: http://www.cogsci.ucsd.edu/~dgroppe/label_vertices.fig If you rotate the figure you can see that some black vertices are interleaved in parts of the label area. thanks again, -David > On Sun, Jun 3, 2012 at 5:23 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >> hmmm, and how are you displaying it in the second (patchy) view? I don't >> think tksurfer fills any holes by default >> >> Bruce >> >> >> On Sun, 3 Jun 2012, David Groppe wrote: >> >>> Thanks for the nigh-instantaneous response Bruce. >>> None of the entries have -1 for a vertex number in the first column >>> (see attached). The smallest value is 75. >>> -David >>> >>> On Sun, Jun 3, 2012 at 5:10 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> wrote: >>>> >>>> do any of the label entries have -1 for a vertex number in the first >>>> column? >>>> If so, tksurfer will sample it onto the surface finding the nearest >>>> surface >>>> vertex. >>>> >>>> >>>> On Sun, 3 Jun 2012, David Groppe wrote: >>>> >>>>> Hi FreeSurfers, >>>>> I am attempting to plot a label in MATLAB using the function >>>>> read_label.m. The label was produced in tksurfer (see >>>>> label_tksurfer.jpg) from a mask created by FSL. When I try to import >>>>> the label into MATLAB via read_label.m, I get the correct number of >>>>> nonzero vertices (i.e., the same number reported by tksurfer when I >>>>> load the label). However the resulting plot is spotty (see >>>>> label_matlab.jpg). I suspect that some vertices that are colored as >>>>> the label in tksurfer are not actually part of the label file (i.e., >>>>> tksurfer is automatically doing some filling in that I'm not aware >>>>> of). Is this true? >>>>> Any tips on how to solve the problem would be greatly appreciated. >>>>> much thanks, >>>>> -David >>>>> >>>>> >>>> >>>> >>>> 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. >>>> >>> >>> >>> >> > > > > -- > David Groppe, Ph.D. > Postdoctoral Researcher > North Shore LIJ Health System > New Hyde Park, New York > http://www.cogsci.ucsd.edu/~dgroppe/ -- David Groppe, Ph.D. Postdoctoral Researcher North Shore LIJ Health System New Hyde Park, New York http://www.cogsci.ucsd.edu/~dgroppe/

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no aseg
by michael kruepke 04 Jun '12

04 Jun '12

Hi all - Having a bit of an issue with trying to run a make_average with the flag --no-aseg. When written make_average_subjects --subject subject1 subject2 --no-aseg --out superaverage the propt runs as if --no-aseg and --out superaverage are subjects i wish to average in with subjects1 and subject2. This is obviously and issue, hoping someone might have an idea of a solution. I have tried moving these flags to somewhere else in the prompt seeing if that would solve it, no luck there. Best- Michael -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkruepke(a)gmail.com (262)-483-7449

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read_label.m produces spotty label (as compared to tksurfer)
by David Groppe 03 Jun '12

03 Jun '12

Hi FreeSurfers, I am attempting to plot a label in MATLAB using the function read_label.m. The label was produced in tksurfer (see label_tksurfer.jpg) from a mask created by FSL. When I try to import the label into MATLAB via read_label.m, I get the correct number of nonzero vertices (i.e., the same number reported by tksurfer when I load the label). However the resulting plot is spotty (see label_matlab.jpg). I suspect that some vertices that are colored as the label in tksurfer are not actually part of the label file (i.e., tksurfer is automatically doing some filling in that I'm not aware of). Is this true? Any tips on how to solve the problem would be greatly appreciated. much thanks, -David -- David Groppe, Ph.D. Postdoctoral Researcher North Shore LIJ Health System New Hyde Park, New York http://www.cogsci.ucsd.edu/~dgroppe/

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Rejoindre mon réseau sur LinkedIn
by subramoniam a via LinkedIn 03 Jun '12

03 Jun '12

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Functional overlay on a surface - interpolation question
by Shay Ohayon 03 Jun '12

03 Jun '12

Hi, I have another silly question. When a functional overlay (say, log p-value map) is loaded to tksurfer, how exactly are the surface vertex values computed? using simple interpolation of the loaded map? or is it something more fancier, like looking along the normal of each surface face and taking the maximum/minimum? The reason I'm asking is because if surface vertices are interpolated exactly using the loaded volume, they don't fall on gray matter (right? either I use the white matter surface or the pial surface, where activation should be in between...) Thanks in advance, Shay Tsao Lab Caltech

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Recent paper on FreeSurfer reliability
by Ed Gronenschild 02 Jun '12

02 Jun '12

Hi, The paper entitled “The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements”, PLoSONE, Vol 7(6), e38234 (2012) may be of interest to all of you. It can be found at: http://dx.plos.org/10.1371/journal.pone.0038234 Cheers, Ed

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