Freesurfer

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30080 discussions

Re: [Freesurfer] deflate compression support
by Pedro Paulo de Magalhães Oliveira Junior 01 Jul '08

01 Jul '08

The problem is if the libtiff was compiled with zlib or not. I think it would be nice to rebuild your libtiff from ports: http://tiff.darwinports.com/ 2008/7/1 Jan Kalkus <jan.francis.kalkus(a)gmail.com>: > I have libtiff 3.8.2. > > On Jul 1, 2008, at 12:06 PM, Pedro Paulo de Magalhães Oliveira Junior > wrote: > > Some versions of LibTiff have the zlib compression support disabled. > > Do you have an older version of LibTiff in your Mac? > > 2008/7/1 Jan Kalkus <jan.francis.kalkus(a)gmail.com>: > >> Hi everyone, >> >> I'm trying to make a monkey template using mris_make_template. So >> far, every time I run the mris_make_template, I get this error: >> >> [jkalkus:~] work% /Volumes/Data/monkey_surface_data/mris_make >> creating new parameterization... >> >> processing subject bu_edited (1 of 1) >> reading spherical surface >> /Volumes/Data/monkey_surface_data//bu_edited/surf/rh.sphere... >> curvature mean = 0.000, std = 1.000 >> computing parameterization for surface >> /Volumes/Data/monkey_surface_data//bu_edited/surf/rh.inflated.H... >> curvature mean = 0.000, std = 0.592 >> computing parameterization for surface >> /Volumes/Data/monkey_surface_data//bu_edited/surf/rh.sulc... >> curvature mean = -0.100, std = 1.787 >> computing parameterization for surface >> /Volumes/Data/monkey_surface_data//bu_edited/surf/rh.smoothwm... >> writing updated template with 1 subjects to monk_temp0.tif... >> monk_temp0.tif: Deflate compression support is not configured. >> TiffWrite: TIFFWriteScanline returned error >> >> I am working on an intel MacBook with OS X 10.5.4 and I'm running >> freesurfer-Darwin-leopard-i686-stable-pub-v4.0.5. Has anyone else >> encountered this problem? Does anyone have any suggestions? Thanks >> >> - Jan Kalkus >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >

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Application error
by Juergen Haenggi 01 Jul '08

01 Jul '08

Dear FS experts I used FS 4.0.3 on a Mac Intel. When I loaded several sig.mgh files as overlays in tksurfer and try to swich between them the following error occurred: can't read "gaHistoWidget(graph)": no such element in array can't read "gaHistoWidget(graph)": no such element in array while executing "Histo_Unzoom $gaHistoWidget(graph)" (procedure "SetOverlayField" line 37) invoked from within "SetOverlayField 1" invoked from within ".w.fwMouseover.fwLabels.fwkLabel_Val2.fwOverlay invoke" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke]" (procedure "tk::ButtonUp" line 22) invoked from within "tk::ButtonUp .w.fwMouseover.fwLabels.fwkLabel_Val2.fwOverlay" (command bound to event) What does it mean? At the beginning I could switch but when trying to switch back the above application error occurred. Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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cortical ribbon back to subject coordinates?
by Dirk Bernhardt-Walther 30 Jun '08

30 Jun '08

Hello The -autorecon2 stage of recon-all generates the binary masks [lr]h.ribbon.mgz. I am assuming that these files are in Talairach space? How can I convert them back to the individual subject's coordinate space? Thanks! Dirk -- ================================= Dirk Bernhardt-Walther, PhD Beckman Postdoctoral Fellow walther(a)uiuc.edu http://netfiles.uiuc.edu/walther/www 5209 Beckman Institute, MC 251 405 N. Mathews Ave. Urbana, IL, 61801 USA phone: +1-217-333-9961 fax: +1-217-333-2922

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dicom to mgz
by Daniel H Choi 30 Jun '08

30 Jun '08

Hi, I am trying to change my dicom files to mgz format. I know recon-all can do this, however after the mgz file is created, tkmedit will not display it. As described in the freesurfer-wiki site, there are steps outlining 2 acquisition directories. What does this specifically refer to? I assumed that I only had one, and therefore entered the following: recon-all -i /mnt/win/MRI_data/MWIN4/O-08-003/DICOM/08021516/33420000/9003-0001-0001-00001.dcm -s O_08_003.mgz The error message said there might be something wrong with the data file (unreadable, or wrong size). Is my command wrong? Thanks. Dan -- Daniel Horim Choi Northwestern University Class of 2009 dhchoi(a)u.northwestern.edu or dchoi1024(a)gmail.com

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Re: About cluster thresholding (fwd)
by Bruce Fischl 30 Jun '08

30 Jun '08

---------- Forwarded message ---------- Date: Mon, 30 Jun 2008 16:23:54 +0100 From: Thomas Nichols <nichols(a)fmrib.ox.ac.uk> To: jorge luis <jbernal0019(a)yahoo.es> Cc: freesurfer(a)nmr.mgh.harvard.edu, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: About cluster thresholding Dear Jorge, When using a permutation procedure, there's no restriction on what initial threshold you use to define clusters (parametric, random field theory, on the other hand, requires a sufficiently high threshold, like P=0.01 or more stringent). As for the number of permutations, see http://www.fmrib.ox.ac.uk/fsl/randomise/ and look for the table of 'Confidence Limits'. There you'll see that the confidence bounds on your P-values depend on nPerms^(-1/2) and the true P-value. For a true P-value of 0.05, you need 5,000 to bring the limits down, and 10,000 to ensure that there is less than a 10% margin of error on a true 0.05 P-value. A couple of caveats, though: The confidence limits / margin of errors assume there is an infinite number of possible permutations, or a very large number. If there are only, say, 1024 possible permutations, there's nothing to be gained from running more (there are no more to run)! Also, since 5,000 or 10,000 will take a long time, I always recommend first running with, say, 100 or 500, just to make sure you've got the right data, have a decent cluster-forming threshold, etc, before running a 'gold standard' number of permutations. -Tom PS: I have to plug my recent work with Steve Smith, on avoiding the problem of 'Which cluster-forming threshold?', with a method called Threshold-Free Cluster Enhancement; see http://www.fmrib.ox.ac.uk/analysis/techrep/tr08ss1/tr08ss1.pdf and http://dx.doi.org/10.1016/j.neuroimage.2008.03.061 . It's currently implemented in FSL's randomise, though is a bit slow. An immenent update to FSL will speed it up considerably. On Mon, Jun 30, 2008 at 4:08 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Jorge, > > I'll leave this for either Doug or Tom Nichols, who understand this much > better than me. I would guess that 5000 is not enough, but I could be wrong. > > cheers, > Bruce > On Mon, 30 Jun 2008, jorge luis wrote: > > Thank you very much Bruce >> >> >> I have another question: >> >> I plan to use permutation testing in order to correct for multiple >> comparisons. >> >> Is it enough to perform 5000 iterations for an initial voxel_wise >> threshold of 0.005? >> >> Is there also any heuristic to select this arbitrary initial threshold and >> theoretical results for the required number of iterations for the >> permutations? >> >> I appreciate very much your help >> >> Jorge >> Phd Student >> >> --- El dom, 29/6/08, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> escribió: >> >> De: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> Asunto: Re: [Freesurfer] About the area of the vertices in the surfaces >>> Para: "jorge luis" <jbernal0019(a)yahoo.es> >>> CC: freesurfer(a)nmr.mgh.harvard.edu >>> Fecha: domingo, 29 junio, 2008 5:22 >>> Hi Jorge, >>> >>> yes, the area of a vertex is 1/3 of the area of all >>> triangles that it is >>> a member of, and it should sum to the area of the surface. >>> The average >>> subject has a correction factor that accounts for the >>> "lost" area due to >>> averaging, so you'll need to apply this if you want it >>> to be in true mm >>> (in the average sense across your subjects). mris_info >>> ~/local_subjects/fsaverage/surf/lh.white >>> reading group avg surface area 864 cm^2 from file >>> Reading in average area >>> /homes/4/fischl/local_subjects/fsaverage/surf/lh.white.avg.area.mgh >>> SURFACE INFO ======================================== >>> type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE >>> num vertices: 163842 >>> num faces : 327680 >>> num strips : 0 >>> surface area: 70394.8 >>> AvgVtxArea 0.429650 >>> AvgVtxDist 0.757401 >>> StdVtxDist 0.227951 >>> group avg surface area: 86444.7 >>> . >>> . >>> . >>> >>> thus, you would need to multiply your areas by >>> 86444.7/70394.8 to get mm in >>> the average cross-subject sense. >>> cheers, >>> Bruce >>> >>> On Sun, 29 Jun >>> 2008, jorge luis wrote: >>> >>> Hello all >>>> I have some questions: >>>> >>>> I would like to know how freesurfer computes the >>>> >>> vertexÿÿs wise areas? eg. thouse in lh.area. >>> >>>> >>>> It should be expected that the sum of the areas of all >>>> >>> the vertices across a surface equals the total surface area? >>> >>>> >>>> To be much specific: >>>> Can I compute the area of an 'activated' >>>> >>> cortical ROI in the average >>> subject by simply adding the area of all its vertices? >>> >>>> >>>> In adavance thank you >>>> >>>> Jorge >>>> Phd Student >>>> >>>> >>>> >>>> >>>> >>>> ¿No te gusta tu dirección de correo? >>>> Consigue una que te guste de verdad - millones de >>>> >>> direcciones de correo disponibles en Yahoo! >>> >>>> http://es.docs.yahoo.com/mail/nueva_direccion.html >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>>> >>>> >>>> >>>> >> >> ______________________________________________ >> Enviado desde Correo Yahoo! La bandeja de entrada más inteligente. >> >> >> -- ____________________________________________ Thomas Nichols, PhD Director, Modelling & Genetics GlaxoSmithKline Clinical Imaging Centre Senior Research Fellow Oxford University FMRIB Centre

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About the area of the vertices in the surfaces
by jorge luis 30 Jun '08

30 Jun '08

Hello all I have some questions: I would like to know how freesurfer computes the vertex’s wise areas? eg. thouse in lh.area. It should be expected that the sum of the areas of all the vertices across a surface equals the total surface area? To be much specific: Can I compute the area of an 'activated' cortical ROI in the average subject by simply adding the area of all its vertices? In adavance thank you Jorge Phd Student ¿No te gusta tu dirección de correo? Consigue una que te guste de verdad - millones de direcciones de correo disponibles en Yahoo! http://es.docs.yahoo.com/mail/nueva_direccion.html

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about thalamus segmentation
by abel cruz vadell 30 Jun '08

30 Jun '08

Hello I have read in some emails about the improvement of the subcortical segmentation in the last FreeSurfer versions. I have 40 subjects processed with the 4.01 version and my attention is focused in the thalamus. Has been improvement the segmentation of this structure in the later FreeSurfer versions? In positive case, is possible to use my 4.01 segmentation in the newer versions or I need to do the overall processing again? Thanks in advance Abel ______________________________________________ Enviado desde Correo Yahoo! La bandeja de entrada más inteligente.

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Massive recon-all.log files
by Sky Raptentsetsang 27 Jun '08

27 Jun '08

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FreeSurfer Stop run autorecon-all at mri_fix_topology Stop run autorecon-all at mri_fix_topology Stop run autorecon-all at mri_fix_topology FreeSurfer stop running at mri_fix_topology with no error message
by Yuan Xu 27 Jun '08

27 Jun '08

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research position in San Francisco, CA
by Brian Roach 27 Jun '08

27 Jun '08

FreeSurfer users, We are looking for new and experienced brain imagers wanting to work in our UCSF-affiliated research lab. Please apply at the following link if interested: http://www.ncire.org/positions.php?id=145 thank you, Brian

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