Freesurfer November 2010

freesurfer@nmr.mgh.harvard.edu

92 participants
127 discussions

clarification regarding total GM and WM volume
by Samantha Clark 06 Nov '10

06 Nov '10

Dear Freesurfer team, I was a little confused by the recent e-mails about total GM and WM. If you could help clarify the below mentioned, I would really appreciate it (am using freesurfer: stable 4 version). 1) For cortical thickness analysis, there is no necessity to normalize each parcellation thickness value 2) For each GM and WM parcellation, we can norrnalize them with the total cerebral cortex volume and WM volume listed in the aseg.stats file 3) If the talairach registration is not the best, its best to not normalize the volumes with the ICV value Thanks so much, Samantha

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Loading two cortical thickness maps simultaneously in TkSurfer or Freeview
by Aly Negreira 06 Nov '10

06 Nov '10

Hi All, I'm sure this is ridiculously simple, but cant seem to load two sig.mgh files (both are cortical thinning maps produced from mri_glmfit) in either TkSurfer or Freeview at the same time. This doesn't seem possible in tksurfer unless i merge the files, which im having trouble figuring out how to do (mri_concat doesnt give me what I want and neither does mri_binarize). I am unclear on how to load sig.mgh files in Freeview and the online guide has yet to create this page. Any advice? Thanks! ALy Machine: Tain Env: dev Files: /space/tain/1/freeview_test/*

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Custom color scale for overlays in tksurfer/freeview
by f.leone＠donders.ru.nl 06 Nov '10

06 Nov '10

Hi everyone, I saw there has been posts on this before, and I know more people here at the center have this request, so I wanted to ask it again, now also for freeview: is it possible to have custom coloring on the surfaces? It is not that I need specific colors, it is just that I find the default coloring not high resolution enough to see anything more than general level differences (e.g., if I have values 0 to 100, I can only see differences between below or above 60 (red vs yellow, plus there is osme dark red for below 40), while I would like to be able to see the gradient and in between values. Or isn't this normal behavior? Can it for example be due to using Virtual GL or due to using double precision values? I just tested using integer data (ranging from 0 to 40) and that was a bit better, but still not as good as I would expect. Anyone any ideas on what I might be doing wrong / whether there is an alternative? kind regards, Frank -- Frank T.M. Leoné, MSc Graduate student | Donders Institute for Brain, Cognition and Behaviour f.leone(a)donders.ru.nl | +31 24 36 12542 / +31 24 36 68388 | Room B.1.31 / Room 1.34

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Re: [Freesurfer] Lobe mapping, based on the Desikan-Killiany Atlas
by rahul＠nmr.mgh.harvard.edu 05 Nov '10

05 Nov '10

Hi Ruthger, The temporal lobe list/label should include the banks of the superior temporal sulcus (bankssts). Not sure why it's not in there but we will include it. Thanks for pointing this out! Best, Rahul > Dear Freesurfers, > > I would like to do Lobe mapping, based on the Desikan-Killiany atlas, see > http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation. > > I was wondering if there is a reason why the banksts is not included in > the list under temporal lobe. My first guess is because this is a sulcus, > but I would like to be sure what is the reason. > > Thank you very much for your suggestions! > > Ruthger Righart (PhD) > > Institute for Stroke and Dementia Research (ISD) > Klinikum der Universität München > Max-Lebsche-Platz 30 > 81377 Munich | Germany > > Ruthger.Righart(a)med.uni-muenchen.de > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Re: [Freesurfer] Voxel-wise T-test
by Douglas N Greve 05 Nov '10

05 Nov '10

gammavar is the "standard" variance (ie, the square of the standard error). The residual variance is in rvar. Mark Hollenbeck wrote: > Hi Doug, > > Thanks again for all your help! — Could you explain gammavar.mgh? Would this be considered the stdev of the results found in gamma.mgh? > > Thanks, > Mark > > On Nov 3, 2010, at 11:17 AM, Douglas N Greve wrote: > > >> right, that is the correlation, not the correlation coefficient >> >> Mark Hollenbeck wrote: >> >>> Hi Doug, >>> >>> Thanks for you help with this. >>> If I am looking for the mean estimated difference (correlation coefficients) between the post-task and pre-task, for certain voxels, would I use gamma.mgh? >>> >>> Thanks, >>> Mark >>> >>> On Nov 1, 2010, at 1:50 PM, Douglas N Greve wrote: >>> >>> >>> >>>> nope, that's an unpaired test. You can do a paired test in one of two ways. >>>> >>>> Method 1: is to create an FSGD file with a class for each subject and one continuous variable. Set this variable to +1 for after task and -1 for before task. Run with DOSS and test the continuous variable. For this test you will need a contrast vector like [0 0 0 ... 0 0 0 1], where the number of zeros equals the number of subjects. In this case, it will best for after>before. >>>> >>>> Mthod 2: do your own subtraction after-before, then run mri_glmfit with --osgm. Warning though: make sure that you create a single mask based on all of the data, not on the subracted data. >>>> >>>> doug >>>> >>>> Mark Hollenbeck wrote: >>>> >>>> >>>>> Hi Doug, >>>>> >>>>> I really appreciate your help. I was able to successfully run this analysis on the surface using the --paired-diff method (mris_preproc). To do this in the volume, however, I'm not quite sure if my methods are accurate. I was hoping you could give me some insight. This is what I did: >>>>> >>>>> For volume, I created a 4D image that contained all subject's data (2 images per subject, so 2*N frames). Created a FSGD file with: >>>>> >>>>> ... >>>>> Input Subject1 before_task >>>>> Input Subject1 after_task >>>>> Input Subject2 before_task >>>>> Input Subject2 after_task >>>>> ... >>>>> Input SubjectN before_task >>>>> Input SubjectN after_task >>>>> >>>>> And used glm_fit, with the 4D volume as --y, my FSGD file (with --allowsubjrep), and a simple contrast of [-1 1]. >>>>> >>>>> Would this method be essentially equivalent to the --paired-diff surface method in mris_preproc/mri_glmfit? Does it account for intra and inter-subject variance? >>>>> >>>>> Thanks. Again, I appreciate your help. >>>>> Mark >>>>> >>>>> On Oct 28, 2010, at 1:48 PM, Douglas N Greve wrote: >>>>> >>>>> >>>>> >>>>>> Hi Mark, yes you can. You'll need to run mri_glmfit with an appropriate FSGD file. Do a search for fsgd on the wiki. Let me know if you get stuck. >>>>>> >>>>>> doug >>>>>> >>>>>> Mark Hollenbeck wrote: >>>>>> >>>>>> >>>>>>> Hi Doug, >>>>>>> >>>>>>> I have two groups of resting state data for a subject population: before a task, and after a task. I would like to do a voxel-wise significance test between the two groups using fsfast, or similar, to find the voxels where there is a statistically significant increase/decrease. Can you help? Thanks! >>>>>>> Mark >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> -- >>>>>> 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 >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> -- >>>> 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 >>>> >>>> >>>> >>>> >>> >>> >>> >> -- >> 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 >> >> >> > > > > -- 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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Questions about event related processing and selxavg-sess and selxavg3-sess
by Katie Bettencourt 05 Nov '10

05 Nov '10

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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Lobe mapping, based on the Desikan-Killiany Atlas
by Righart, Ruthger Dr. 05 Nov '10

05 Nov '10

Dear Freesurfers, I would like to do Lobe mapping, based on the Desikan-Killiany atlas, see http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation. I was wondering if there is a reason why the banksts is not included in the list under temporal lobe. My first guess is because this is a sulcus, but I would like to be sure what is the reason. Thank you very much for your suggestions! Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany Ruthger.Righart(a)med.uni-muenchen.de

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mri_glmfit-sim on longitudinal data
by Nicki Langer 05 Nov '10

05 Nov '10

Hi, I have read the Freesurfer Tutorial, but there is still something I do not understand. I want to run the mri_glmfit-sim command on our data. I have one sample (10 subjects), which were examined at 2 different timepoints. I tried to use this command: mri_glmfit-sim --glmdir Plast_injury_Thickness_LH_sensorimotor.glmdir --sim mc-z 1000 2 lh_mz-z.abs --sim-sign abs --overwrite The following error message occured: y has 10 inputs, X has 20 Rows. Although the X-file has only 10 rows (here is the content of the X file an y file) X.mat = 1 1 1 1 1 1 1 1 1 1 y.fsgd = GroupDescriptorFile 1 Title InjuryInducedChanges MeasurementName external Tessellation surface PlotFile /Applications/freesurfer/subjects/average/stats/glm/Plast_injury_lh_thickness.15.mgh DesignMatFile X.mat dods DeMeanFlag -1 ResidualFWHM 18.070986 LogY 0 Class injury Input PlastInjur01_tp1.long.PlastInjur01 injury Input PlastInjur01_tp2.long.PlastInjur01 injury Input PlastInjur02_tp1.long.PlastInjur02 injury Input PlastInjur02_tp2.long.PlastInjur02 injury Input PlastInjur03_tp1.long.PlastInjur03 injury Input PlastInjur03_tp2.long.PlastInjur03 injury Input PlastInjur04_tp1.long.PlastInjur04 injury Input PlastInjur04_tp2.long.PlastInjur04 injury Input PlastInjur05_tp1.long.PlastInjur05 injury Input PlastInjur05_tp2.long.PlastInjur05 injury Input PlastInjur06_tp1.long.PlastInjur06 injury Input PlastInjur06_tp2.long.PlastInjur06 injury Input PlastInjur07_tp1.long.PlastInjur07 injury Input PlastInjur07_tp2.long.PlastInjur07 injury Input PlastInjur08_tp1.long.PlastInjur08 injury Input PlastInjur08_tp2.long.PlastInjur08 injury Input PlastInjur09_tp1.long.PlastInjur09 injury Input PlastInjur09_tp2.long.PlastInjur09 injury Input PlastInjur010_tp1.long.PlastInjur010 injury Input PlastInjur010_tp2.long.PlastInjur010 injury Creator mri_glmfit SUBJECTS_DIR /Applications/freesurfer/subjects SynthSeed 1289388591 What is exactly wrong? Or how do I apply the mri_glmfit-sim for longitudinal data correctly. Thanks a lot for your help. Best regards, Nicolas -- Nicolas Langer MSc.UZH (lic. phil.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, 8050 Zurich, Switzerland 0041 44 635 73 92 (phone office) 0041 76 422 46 45 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) nicolas.langer[at]uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website)

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select_talairach_point
by Arslan, Ali 05 Nov '10

05 Nov '10

Hi, I would like to go over a list of talairach coordinates (which describe my electrode locations) and send these vertices as labels. I'm using select_talairach_point function, but the problem is that it only keeps the latest selection. So I end up with just one vertex. I'm using this TCL script that I wrote: set f [ open "/Users/aarslan/Desktop/talcoord.txt" ] set a [read $f] set b [split $a "\n"] set i 0 foreach j $b { select_talairach_point [lindex $j 0] [lindex $j 1] [lindex $j 2] puts "[lindex $j 0] [lindex $j 1] [lindex $j 2]" incr i } Is there a way to store multiple vertices as a label or annotation? Or at least keep the previously selected vertices during each iteration? Best, -- Ali B. Arslan Cognitive, Linguistic and Psychological Sciences Brown University

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talairach.xfm and talairach_avi
by Lisa F. Akiyama 04 Nov '10

04 Nov '10

Hello, Are there any documentations on the details of the talairach_avi command and the 3x4 matrix (talairach.xfm) output? Thank you. Best, Lisa Akiyama ______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington <lrisa87(a)uw.edu> P Please consider the environment before printing this e-mail.

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Freesurfer November 2010