Freesurfer June 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

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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Poor Long Cortical Reconstruction
by Jeff Sadino 01 Jun '12

01 Jun '12

Hello FreeSurfers, I have a weird longitudinal surface reconstruction. The other long timepoint surfaces look fine. The base surfaces look fine. On this subject, the files up to surface reconstruction look fine. However, then the surface gets all out of alignment. Does anyone have any suggestions for why this would happen? Thank you, Jeff Sadino

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Using QDEC ROIs to extract text files of surface areas
by Cynthia Elisabeth Krafft 01 Jun '12

01 Jun '12

Hello, Sorry for the newbie question. I completed a group analysis in QDEC and drew a ROI, which I saved and mapped to the individual subjects. I'm interested in getting text output of the surface area for each individual within that ROI. Here is an example of the command that I ran for one person: mris_anatomical_stats -l lh.X.area.label -b -nsmooth 15 subject lh white The problem is that when I plot these values against the variable that I originally put in to the analysis (for which I got significant results in this ROI in QDEC), it doesn't look like there is anything there, so I guess I did something wrong or my interpretation is wrong. I'd appreciate any insight! Thanks, Cindy

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Re: [Freesurfer] mri_surf2surf error
by mdkruepke＠uwalumni.com 01 Jun '12

01 Jun '12

Actually one last question- I used label2label to transfer some labels and grab ROI thickness averages from the labels on the subject with the rh.cortex.label that has been overwritten. I received no errors during this, does this mean that the label transfers and averages are valid, or do i need to redo them? Best- Michael > On Fri, Jun 1, 2012 at 11:05 AM, mdkruepke(a)uwalumni.com < > mdkruepke(a)uwalumni.com> wrote: > >> Doug - >> >> That does indeed seem to be the problem! Ill just rerun some things here >> to rectify that. Thanks for all the help everyone! >> >> Best- >> Michael >> >> On Fri, Jun 1, 2012 at 11:01 AM, Douglas N Greve < >> greve(a)nmr.mgh.harvard.edu> wrote: >> >>> I think the label file got overwritten at some point. Check the time >>> stamp and see if it is much different than the other rh files >>> >>> On 06/01/2012 11:55 AM, mdkruepke(a)uwalumni.com wrote: >>> > Bruce- >>> > >>> > It is, and i agree, for instance here is the lh.cortex.label file >>> > >>> > #label , from subject ?? >>> > 149955 >>> > 22 -10.374 55.016 3.203 0.0000000000 >>> > 112 -6.294 36.386 -7.809 0.0000000000 >>> > 114 -6.137 38.556 13.808 0.0000000000 >>> > 247 -11.304 45.214 -2.709 0.0000000000 >>> > 248 -6.278 39.973 2.192 0.0000000000 >>> > 249 -10.766 45.545 6.476 0.0000000000 >>> > 507 -11.087 42.990 18.865 0.0000000000 >>> > >>> > On 6/1/12, Bruce Fischl<fischl(a)nmr.mgh.harvard.edu> wrote: >>> >> that is the rh.cortex.label file? It doesn't look like it.... >>> >> >>> >> On Fri, 1 Jun 2012, mdkruepke(a)uwalumni.com >>> >> wrote: >>> >> >>> >>> Bruce- >>> >>> >>> >>> Here you go. Subjects recoded. >>> >>> >>> >>> Graph: name >>> >>> >>> >>> Data: path >>> >>> Variable: Subject >>> >>> Measurement: external >>> >>> subject id, class id, variable value, measurement value, standard >>> >>> deviation >>> >>> ------------ >>> >>> S1 Cl1 0.0 3.10522500831 0.268702566292 >>> >>> S2 Cl1 1.0 2.67585065105 0.396833961125 >>> >>> S3 Cl1 2.0 3.07631433273 0.173949345568 >>> >>> S4 Cl1 3.0 2.85668014067 0.0907729539181 >>> >>> S5 Cl1 4.0 3.24184323479 0.212597547853 >>> >>> S6 Cl1 5.0 2.54176559894 0.111183384791 >>> >>> S7 Cl1 6.0 2.87165045086 0.137271513295 >>> >>> S8 Cl1 7.0 2.72165358457 0.128648203321 >>> >>> >>> >>> On 6/1/12, Bruce Fischl<fischl(a)nmr.mgh.harvard.edu> wrote: >>> >>>> something like this: >>> >>>> >>> >>>> head ~/local_subjects/bruce/label/rh.cortex.label >>> >>>> #!ascii label , from subject vox2ras=TkReg >>> >>>> 141813 >>> >>>> 0 11.129 -93.761 -16.820 0.0000000000 >>> >>>> 1 11.136 -93.912 -16.623 0.0000000000 >>> >>>> 2 10.755 -93.913 -16.573 0.0000000000 >>> >>>> 3 11.696 -93.374 -17.237 0.0000000000 >>> >>>> 4 11.022 -93.203 -16.969 0.0000000000 >>> >>>> 5 11.020 -93.855 -17.042 0.0000000000 >>> >>>> 6 10.248 -93.745 -16.712 0.0000000000 >>> >>>> 7 11.591 -93.603 -17.551 0.0000000000 >>> >>>> >>> >>>> >>> >>>> >>> >>>> and please cc the list so others can answer! >>> >>>> On Fri, 1 Jun 2012, >>> >>>> mdkruepke(a)uwalumni.com wrote: >>> >>>> >>> >>>>> Bruce- >>> >>>>> The partition does not appear to be full, although we have been >>> having >>> >>>>> issues with migrating data so >>> >>>>> that could be a source of the issue. The rh.cortex.label does >>> exist and >>> >>>>> is >>> >>>>> located within the subject's >>> >>>>> label dir. As for the first couple of lines, I am unsure what you >>> are >>> >>>>> asking for. >>> >>>>> >>> >>>>> Thanks for the quick response! >>> >>>>> >>> >>>>> Best- >>> >>>>> Michael >>> >>>>> >>> >>>>> On Fri, Jun 1, 2012 at 10:26 AM, Bruce Fischl >>> >>>>> <fischl(a)nmr.mgh.harvard.edu> >>> >>>>> wrote: >>> >>>>> Hi Michael >>> >>>>> >>> >>>>> can you check to see that your partition is not full? Does >>> the >>> >>>>> rh.cortex.label file exist >>> >>>>> in that subject's label dir? If so, what are the first >>> couple of >>> >>>>> lines? >>> >>>>> >>> >>>>> cheers >>> >>>>> Bruce >>> >>>>> >>> >>>>> On Fri, 1 Jun 2012, mdkruepke(a)uwalumni.com wrote: >>> >>>>> >>> >>>>> To anyone who can help - >>> >>>>> I am trying to tun a GLM on a set of data and am >>> currently >>> >>>>> receiving an error >>> >>>>> during the mri_surf2surf >>> >>>>> portion. When running this portion i receive an error >>> ( >>> >>>>> could >>> >>>>> not scan # of >>> >>>>> lines from (path to >>> >>>>> rh.cortex.label)). This does not happen when running >>> this >>> >>>>> portion for the lh, >>> >>>>> only the right. I am >>> >>>>> unable to find any information on this error on the >>> mailing >>> >>>>> list so im hoping >>> >>>>> someone can help! >>> >>>>> >>> >>>>> Best- >>> >>>>> Michael Kruepke >>> >>>>> >>> >>>>> -- >>> >>>>> Michael D. Kruepke >>> >>>>> PhD - University of Illinois at Urbana-Champaign >>> >>>>> BA - Psych - University of Wisconsin-Madison >>> >>>>> mdkruepke(a)gmail.com >>> >>>>> (262)-483-7449 >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> 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. >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> -- >>> >>>>> Michael D. Kruepke >>> >>>>> PhD - University of Illinois at Urbana-Champaign >>> >>>>> BA - Psych - University of Wisconsin-Madison >>> >>>>> mdkruepke(a)gmail.com >>> >>>>> (262)-483-7449 >>> >>>>> >>> >>>>> >>> >>>>> >>> >>> >>> >>> >>> > >>> >>> -- >>> 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 >>> >> >> >> >> -- >> Michael D. Kruepke >> PhD - University of Illinois at Urbana-Champaign >> BA - Psych - University of Wisconsin-Madison >> mdkruepke(a)gmail.com >> (262)-483-7449 >> >> > > > -- > Michael D. Kruepke > PhD - University of Illinois at Urbana-Champaign > BA - Psych - University of Wisconsin-Madison > mdkruepke(a)gmail.com > (262)-483-7449 > > -- 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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Freesurfer June 2012