Freesurfer June 2008

freesurfer@nmr.mgh.harvard.edu

58 participants
77 discussions

mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm
by PKUNWAR＠nmr.mgh.harvard.edu 26 Aug '09

26 Aug '09

Hi all, I was going through the FSFAST TUTORIAL from wiki( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial?action=highlight&v…) I got the follwoing error during mri_volcluster, "NOT Adjusting threshold for 1-tailed test ERROR: you must specify a pos or neg sign with --fwhm" I have fwhm.dat file with 4. something vlaue. Command used, [galen:odd-v-0] (nmr-std-env) mri_volcluster --in tal.rfx.osgm/osgm/sig.nii --thmin 2 --fwhmdat tal.rfx.osgm/fwhm.dat --cwpvalthresh 0.1 --mask tal.rfx.osgm/mask.nii --fsaverage --sum tal.rfx.osgm/osgm/cluster.sum --cwsig tal.rfx.osgm/osgm/cwsig.cluster.nii --out tal.rfx.osgm/osgm/sig.cluster.nii --ocn tal.rfx.osgm/osgm/ocn.cluster.nii without --fwhmdat flag, it gave me another error "ERROR: need csd with --cwsig" will appreciate for help thanks pratap ----------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20070927 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_003/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/subjects PWD: /space/galen/3/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/fb1-preproc-study/group-analysis-tut/sm-gamma-fwhm5/odd-v-0

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design matrix : inter-run effetcs
by Andersson Frederic 02 Dec '08

02 Dec '08

Hi, Computing individual fMRI analysis (several runs) and looking at the design matrix (X.mat), I saw that only one regressor represents each condition. I was expecting that the number of regressors concerning a condition would be the number of runs (as SPM). There are "inter-run effect" regressors but is this better if I affect a different value for each of run and each condition (see examples below). Other question concerning design matrix : only 3 movement parameters included in the design matrix. Why 3 rather than the 6 computed during movement correction? Concerning inter-run effects and movement parameters, is there any advantage of reducing the number of regressors but having a less ideal model? >>> 1 condition = 1regressor 0 = rest 1=conditionA 2=conditionB Pardagim files : RUN#1 RUN#2 RUN#3 0 0 0 0 0 0 3 0 3 0 3 0 6 0 6 0 6 0 9 0 9 0 9 0 12 0 12 0 12 0 15 1 15 1 15 1 18 1 18 1 18 1 21 1 21 1 21 1 24 1 24 1 24 1 27 1 27 1 27 1 30 0 30 0 30 0 33 0 33 0 33 0 36 0 36 0 36 0 39 0 39 0 39 0 42 2 42 2 42 2 45 2 45 2 45 2 48 2 48 2 48 2 51 2 51 2 51 2 54 2 54 2 54 2 57 0 57 0 57 0 >>> 1 condition = 1regressor / run 0=rest 1=conditionA run#1 2=conditionB run#1 3=conditionA run#2 4=conditionB run#2 5=conditionA run#3 6=conditionB run#3 Pardagim files : RUN#1 RUN#2 RUN#3 0 0 0 0 0 0 3 0 3 0 3 0 6 0 6 0 6 0 9 0 9 0 9 0 12 0 12 0 12 0 15 1 15 3 15 5 18 1 18 3 18 5 21 1 21 3 21 5 24 1 24 3 24 5 27 1 27 3 27 5 30 0 30 0 30 0 33 0 33 0 33 0 36 0 36 0 36 0 39 0 39 0 39 0 42 2 42 4 42 6 45 2 45 4 45 6 48 2 48 4 48 6 51 2 51 4 51 6 54 2 54 4 54 6 57 0 57 0 57 0 Frédéric ANDERSSON.

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Checking for spikes
by Brittany Cassidy 06 Aug '08

06 Aug '08

Hello all, I was looking for a general way to check for spiking from Freesurfer or the FSFast stream. Any ideas are appreciated. Thanks! -Brittany

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IO with freesurfer files (.mgh in particular) from Python
by Yaroslav Halchenko 21 Jul '08

21 Jul '08

Does anyone know any handy module to at least read in .mgh files from Python? Or should I simply try mri_convert them into .minc and use netcdf module within python? Thanks in advance for the ideas! -- Yaroslav Halchenko Research Assistant, Psychology Department, Rutgers-Newark Student Ph.D. @ CS Dept. NJIT Office: (973) 353-5440x263 | FWD: 82823 | Fax: (973) 353-1171 101 Warren Str, Smith Hall, Rm 4-105, Newark NJ 07102 WWW: http://www.linkedin.com/in/yarik

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Talairach coordinates
by Feng-Xian Yan 08 Jul '08

08 Jul '08

Hi, I have some problems about surface coordinates. After running the qdec and analyzed my data(cortical thickness), I display a plot of the data for a particular vertex by left-clicking on a point while holding down the Ctrl key. It shows a plot and its plot window shows this vertex's *surface coordinates.* 1) Does the surface coordinates differ from Talairach coordinates? 2) If yes, can I translate the surface coordinates to Talairach coordinates? And how do I do? Does Freesurfer have some methods to do that? Thank you in advance. Feng-Xian

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orientation problem when converting from SPM .nii format to bshort
by Leila Reddy 07 Jul '08

07 Jul '08

Hi, I am trying to convert SPM5 .nii files into bshort and I used the following command: mri_concat fkoch-0007*.nii --o bold/007/fspm_000.bshort The command seems to work in that I have a bunch of bshort files in my bold/007 directory but when I try to view the slices (using sliceview-sess for example) the slices are all upside-down (rotated by 180 degrees). Is there an option I can use to get them the right side up? I'm using FS v3 on an IntelMac and my version of mri_concat is stable3. Here is the output of bugr: --------------------------------------------------------------------- FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5 Kernel info: Darwin 8.11.1 i386 --------------------------------------------------------------------- Thanks, Leila

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documentation of the Freesurfer output and directory structure?
by Turner, Jessica 02 Jul '08

02 Jul '08

Hi experts-I have to document for some non-Freesurfer users what is in all the Freesurfer 3.05 subdirectories from an analysis. We have come up with a lot of it from the Wiki pages and tutorials, but there are some things that still aren't clear (what exactly is the bem directory for? What exactly is the mri_nu_correct.mni.log file? Etc.). Is it laid out clearly somewhere? I've seen the pages about which files are created by what process, etc. and it seems like it should say somewhere what these directories and files really are, I'm just missing it. Thanks, Jess ------------------------ Jessica Turner, Ph.D. Project Manager, FBIRN (www.nbirn.net) Department of Psychiatry and Human Behavior University of California, Irvine Phone: (949) 824-3331 Fax: (949) 824-3324

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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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Freesurfer June 2008