Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

graph average ROI
by Juranek, Jenifer 18 Feb '09

18 Feb '09

Hi, I'm running fsv420 on RHEL4. Within the qdec module (v1.2) menu options, View, Graph the ROI --> generates average +/- SD or SE? Many Thanks, Jenifer

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Group Cortical Thickness
by Jeff Sadino 18 Feb '09

18 Feb '09

Hello, I want to run group statistics on the cortical thickness for a study with 3 groups, each with about 30 subjects. To do this, I need to create an average cort thickness map for each group. We are interested in basic statistics, so nothing too advanced. I am wondering what would be the most efficient way to go about this. From what I can tell, FsFast is the program used to do group analysis. Would it be fastest to learn FsFast to process all my group data, or I am thinking since we only need basic stats, it may be faster and easier to register each subject's ?h.thickness file to an average sphere and then load the registered thickness file into matlab to do the stats? I think I would need to modify the commands from auto-recon stage 3 to use the thickness file, for example: mris_sphere ?h.thickness ?h.thickness.sphere mris_register -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.thickness.sphere.reg mris_jacobian ?h.white ?h.thickness.sphere.reg ?h.jacobian_white mrisp_paint -a 5 $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#6 ?h.thickness.sphere.reg ?h.thickness.avg_curvWe have a cluster, so the processing could be done fairly quickly. Thank you in advance for your advice! Jeff Sadino _________________________________________________________________ Stay up to date on your PC, the Web, and your mobile phone with Windows Live. http://clk.atdmt.com/MRT/go/msnnkwxp1020093185mrt/direct/01/

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permutation / mc-z simulation failure?
by Burmicz, Ryzarda 18 Feb '09

18 Feb '09

Hello, I have just run a number of permutation and mc-z on data that was previously analysed using qdec. Unfortunately none of my clusters reach significance (in some cases there are no clusters found at all) and I am unsure as to what I am doing wrong. I am running freesurfer v4.1.0 on CentOS. My commands were as follows: mri_glmfit –y y.mgh –fsgd ./qdec.fsgd dods --surf fsaverage lh --fwhm 15 –glmdir ./glmdir --C ./contrasts/lh-Diff-patient-CONTROL-Intercept-thickness.mat --sim perm 5000 2 ./glmdir/csd1 followed by: mri_surfcluster --in ./lh-Diff-patient-CONTROL-Intercept-thickness/sig.mgh –csd ./glmdir/csd1-lh-Diff-patient-CONTROL-Intercept-thickness.csd --sum lh-Diff-patient-CONTROL-Intercept-thickness/sig.cluster.sum –cwsig lh-Diff-patient-CONTROL-Intercept-thickness/sig.cluster.mgh I append a log file of mri_glmfit and the output of mri_surfcluster below – there are clusters listed but none of them reach significance. It is confusing because I was under the impression that permutation thresholding was less conservative than fdr correction. I have also run these using –sim mc-z 5000 2 - maybe I am not performing enough iterations? Also: is RFT correction implemented in the latest version of freesurfer? Any help appreciated, Rysia mri_glmfit logfile: $Id: mri_glmfit.c,v 1.138.2.3 2008/08/27 13:33:05 greve Exp $ cwd /cns_zfs/sphasas cmdline mri_glmfit --y /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15/y.mgh --fsgd /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15/qdec.fsgd dods --glmdir /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15 --surf fsaverage rh --label /cns_zfs/sphasas/fsaverage/label/rh.cortex.label --C /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15/contrasts/rh-Avg-Intercept-thickness.mat --C /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15/contrasts/rh-Diff-OCD-CONTROL-Intercept-thickness.mat sysname Linux hostname haemoglobin.cns.image.iop machine x86_64 user kkvi1114 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15/y.mgh logyflag 0 usedti 0 FSGD /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15/qdec.fsgd labelmask /cns_zfs/sphasas/fsaverage/label/rh.cortex.label maskinv 0 glmdir /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15 DoFFx 0 ResidualFWHM 18.998058 SearchSpace 75188.635931 anattype surface Output of mri_surfcluster: cwd /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15 # sysname Linux # hostname haemoglobin.cns.image.iop # machine x86_64 # FixVertexAreaFlag = 1 # # Input ./lh-Diff-OCD-CONTROL-Intercept-thickness/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # SUBJECTS_DIR /software/system/freesurfer/freesurfer-4.1.0/subjects # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 5000 # CSD simtype perm # CSD contrast lh-Diff-OCD-CONTROL-Intercept-thickness # CSD confint 90.000000 # Overall max 2.18803 at vertex 126138 # Overall min -2.94444 at vertex 75849 # NClusters 6 # Total Cortical Surface Area 65416.6 (mm^2)‏ # FixMNI = 1 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs 1 -2.944 75846 61.98 -17.6 -37.0 -4.2 0.84860 0.84200 0.85500 142 2 -2.672 22094 96.92 -29.6 0.5 -24.2 0.80680 0.79960 0.81400 182 3 2.188 126138 41.24 -22.1 -56.8 40.5 0.87160 0.86560 0.87760 74 4 2.095 81711 45.09 -32.4 -38.2 39.4 0.86860 0.86240 0.87480 105 5 2.061 147756 12.32 -6.2 -61.7 38.4 0.90520 0.89980 0.91040 20 6 2.001 133188 0.60 -32.0 -44.7 59.0 0.91660 0.91160 0.92160 1

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mris_divide_parcellation with same area
by Jose Luis Cantero Lorente 18 Feb '09

18 Feb '09

Dear FS Team, I used mris_divide_parcellation to create a new parcelation with smaller regions, but they result in different sizes. I would need to get smaller cortical parcellated regions, but all of them with similar areas. How can I get it? Could I decide the area size of each new parcellated region? Thank you in advance. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/en/

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Manual segmentation
by Kelly Silva 18 Feb '09

18 Feb '09

Hello, I´d like to know what´s the comand to save the new manual segmentations of the subcortical structures. Thanks, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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Re: [Freesurfer] Qdec area measure
by Darren Gitelman 18 Feb '09

18 Feb '09

Devdutta, Nick, Bruce, Mike I'm trying to understand these measures in terms of how they would map to the brain physically. Would it be correct that the size of the triangles touching a vertex would be related to the amount curvature near a particular vertex and therefore the amount of unfolding that takes place? Thus surface area would seem to relate to both brain size and the foldiness of the brain, and brain size could relate to a variety of factors including the cortical thickness but also the amount of underlying white matter. So overall surface area seems to be a complex metric that could reflect changes in underlying white matter, cortical thickness and foldiness. Is this correct? I guess one would have to correct for overall brain size (using TIV or similar measure as a covariate) when examining surface area because of the effect of amount of gray and/or white matter. Volume then would be the amount of cortex underlying a vertex and the triangles connected to it (estimated as an average of the pial and white matter surface areas). Darren > I think the area probably should be corrected to preserve the native area >>> of the subject, but as you say we haven't gotten to the correction yet. On >>> Tue, 17 Feb 2009, Nick Schmansky wrote: >>> >>> Devdutta, >>> >>> The 'area' of a vertex on a surface in freesurfer is just the average >>> of >>> the area of the triangles which touch that vertex . >>> >>> The volume data associated with a vertex created for a subject is not >>> buggy in how it is calculated now. it is the area of the mid-point >>> between the white and pial surfaces times the thickness at the vertex. >>> The question that has been bandied about internally is whether this >>> volume calculation should be corrected when it is mapped to the >>> fsaverage surface during a group analysis (qdec does this mapping of >>> the >>> volume calcs of each subject to the fsaverage surface, when you select >>> 'volume' as one of the measures). At some point we will visit this >>> issue (and determine if it is an issue) but other stuff seems to take >>> priority. Maybe someone on the list can chime in. >>> >>> Nick >>> >>> On Tue, 2009-02-17 at 11:28 -0600, Devdutta W wrote: >>> >>> Hi, >>> In Qdec, what exactly does the area option measure? As I >>> understand, >>> qdec does its calculations vertex by vertex, which makes sense in >>> case >>> of cortical thickness. But if area refers to surface area how >>> does >>> that change from vertex to vertex? Or is it calculating the area >>> by >>> ROI? Is my understanding of this correct? >>> >>> Also, as regards to the volume option, I was told that it is not >>> working. But when I ran it it seems to work fine. Should I take >>> that >>> to mean that the calculation has bugs and that the results it >>> displays >>> are incorrect? Or has it been fixed? >>> >>> I greatly appreciate any help in this matter. >>> >>> Thank you, >>> Devdutta >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>>

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RE: [Freesurfer] brazil course
by ppj＠netfilter.com.br 17 Feb '09

17 Feb '09

We still have four places. Sent from my Nokia phone -----Original Message----- From: Nick Schmansky Sent: 17/02/2009 18:36:08 To: Sam Torrisi Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] brazil course Sam, Pedro Paulo de M. Oliveira's email is: ppj at netfilter.com.br The original post is here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009- February/009688.html with details here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/BrazilCourseSchedule A course is being offered in Boston in April, but its already full. You can register for it anyway to be put on the waiting list for that course or future courses. That course description and link to the registration page is here: http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription There will likely be a one-day Freesurfer component to an FSL course that might be offered in San Francisco just before HBM in June, but you'll have to monitor the FSL site to check on the status of that (and noting that the Freesurfer component is not separate from the main FSL course). Nick On Tue, 2009-02-17 at 13:11 -0800, Sam Torrisi wrote: > hello there, > > i have questions for Pedro Paulo de M. Oliveira regarding the upcoming > Brazilian FS course but cannot find his email address anywhere in the > archives or his announcement. also, do you know if there is another > upcoming course in the states, preferably on the west coast? thank you > > -Sam Torrisi > > Neuroscience IDP PhD student > University of California Los Angeles > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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% threshold in mri_segment
by Bai Xue 17 Feb '09

17 Feb '09

Hi, What's the use of the % threshold (-p option) in mri_segment? Thanks. Bai

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brazil course
by Sam Torrisi 17 Feb '09

17 Feb '09

hello there, i have questions for Pedro Paulo de M. Oliveira regarding the upcoming Brazilian FS course but cannot find his email address anywhere in the archives or his announcement. also, do you know if there is another upcoming course in the states, preferably on the west coast? thank you -Sam Torrisi Neuroscience IDP PhD student University of California Los Angeles

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(no subject)
by carl＠nmr.mgh.harvard.edu 17 Feb '09

17 Feb '09

As far as the first, This happens sometimes when you make your own average subject. You just need to inflate it more. I will try to dig up an old email I have on the commands. As for the second, just click the redraW BUTTON CARL SCHWARTZ On 2/17/09 12:44 PM, "Devdutta W" <devdutta.w(a)gmail.com> wrote: Oops, forgot the attachment. On Tue, Feb 17, 2009 at 11:42 AM, Devdutta W <devdutta.w(a)gmail.com> wrote: Hello again, My questions refer to the attached image. The image is of the average subject I created from our subjects using the "make_average_subject" command. As you can see, in an inflated view there are many gyri and sulci looking structures that shouldn't be there. Clearly something is not right. My first question is what aspect of our subjects' brains could be causing this? I have inspected the brains in tksurfer and have not found any defects that could account for this. My second question refers to the oddness at the bottom left of the image. That is something I notice happening all the time. Everytime I drag any window across the tksurfer or tkmedit window that happens. It goes away once I rotate the brain or zoom in or out or anything like that. Is this something that people have encountered before or is this an anomaly unique to our system? Once again, I really appreciate any help these matters. Thank you, Devdutta

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