Freesurfer March 2009

freesurfer@nmr.mgh.harvard.edu

73 participants
100 discussions

LGI error in make_outer_surface at 31
by Juranek, Jenifer 07 Apr '11

07 Apr '11

Hi, Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB v7.6.0.324 (R2008a) installed. Subject was processed under fsv405. Specific error is pasted below: Any suggestions to correct my error? Thanks, Jenifer >> reading filled volume... closing volume... ??? Undefined function or method 'fspecial' for input arguments of type 'char'. Error in ==> make_outer_surface at 31 Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008 [jjuranek@localhost jjuranek_fsv405]$

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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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Multiple Comparison - Clusterwise Correction
by Devdutta W 01 Jul '09

01 Jul '09

Hi Freesurfers, More questions about this analysis. 1) Referring to the documentation, we used the following command: tksurfer fsaverage lh inflated -annot mc-z.abs.2.sig.ocn.annot -fthresh 2 -curv -gray The documentation says we should see an image as shown in Figure 1 (attached). But what we see is Figure 2 (also attached). Can somebody explain this? 2) When running the simulation does it matter what threshold we use? For example, can we use a threshold of 2 or 3 (instead of 4 as shown in documentation) when running mri_glmfit-sim? And do we have to use the same threshold while displaying the clusters after? Thanks for any help. Devdutta

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postdoc position
by Elizabeth Mormino 11 May '09

11 May '09

Dear Freesurfer community: Postdoctoral positions are available in the Jagust Lab in the Helen Wills Neuroscience Institute at the University of California, Berkeley. We are studying brain aging using PET, structural MRI and fMRI. One project uses PET to measure brain beta-amyloid accumulation with the amyloid imaging agent PIB and relates these biochemical measurements to changes in brain structure and function. Another project uses PET measures of dopamine function and dopamine release with raclopride, and relates dopamine release to brain activation and working memory performance using fMRI. The goal of these projects is to understand how biochemistry affects frontal and medial temporal lobe working and episodic memory systems in aging. Please contact William Jagust: jagust(a)berkeley.edu for more information.

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3D visualization of subcortical volumes
by Alexa Nardelli 11 Apr '09

11 Apr '09

Hi, I have used FreeSurfer volumetrics to obtain various volumes of some subcortical structures. I would like to obtain a 3D image of each of these subcortical structures. I have tried importing the volumes into Matlab, however Matlab doesn't recognize the mgz file. Any suggestions on how I could go about doing this? Thanks, Alexa

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tksurfer Load Group Descriptor File error
by Jeff Sadino 07 Apr '09

07 Apr '09

Hello, Can someone help me get scatterplots of my data? I am using freesurfer 3.0.5. I have ran these commands: mris_preproc --fsgd try1.fsgd --target fsaverage --hemi lh --meas thickness --out lh.try1.mgh mri_surf2surf --hemi lh --s fsaverage --sval lh.try1.mgh --fwhm 10 --tval lh.try1.fw.mgh mri_glmfit --y lh.try1.fw.mgh --fsgd try1.fsgd dods --C try1.mtx --surf fsaverage lh --glmdir lh.try1.dir tksurfer fsaverage lh inflated -annot aparc.atlas2005_simple -overlay lh.try1.dir/try1.mtx/sig.mgh Then selected a vertex, then File->Load Group Descriptor File and selected try1.fsgd, but I get this error: WARNING: Marker for class ctrl was invalid. WARNING: Color for class ctrl was invalid. WARNING: Marker for class cd was invalid. WARNING: Color for class cd was invalid. This is try1.fsgd: GroupDescriptorFile 1 Title try1 MeasurementName thickness Class ctrl Class cd Variables Age Input 040004_P02 ctrl 55.18 Input 050046_S02 ctrl 37.45 ... ... Input 070073_S01 cd 20.54 Input 070114_OGM01 cd 46.03 I also tried with lh.try1.dir/y.fsgd, but get a similar error: INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: gdfRead: reshaping WARNING: Marker for class ctrl was invalid. WARNING: Color for class ctrl was invalid. WARNING: Marker for class cd was invalid. WARNING: Color for class cd was invalid. y.fsgd looks like this: GroupDescriptorFile 1 Title try1 MeasurementName external Tessellation surface PlotFile /data/Jeff/glmtut/pass5/try1/lh.try1.fw.mgh DesignMatFile fsgd.X.mat dods ResidualFWHM 22.331472 Class ctrl Class cd Variables Age Input 040004_P02 ctrl 55.18 Input 050046_S02 ctrl 37.45 ... ... Input 070073_S01 cd 20.54 Input 070114_OGM01 cd 46.03 Creator mri_glmfit SUBJECTS_DIR /share/apps/freesurfer/subjects SynthSeed 1237057379 In both cases, a graph pops up, but it is blank. Thank you in advance for your suggestions, Jeff Sadino _________________________________________________________________ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_70faster_032009

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microparcellation
by Jose Luis Cantero Lorente 05 Apr '09

05 Apr '09

Dear Freesurfers, We are trying to subdivide the cortical surface of our average subject into a set of small and compact regions of similar area. Please have a look to the attached file (taken from Hagmann et al. (2008) in PLoS Biol) to have a better idea what I would like to get. We tried it hard by using different strategies, but results were not as expected. Could anybody give me some insights about how to approach this problem by using Freesurfer or Matlab code? Thank you very much 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/es/

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Command works in optseq, not optseq2
by Dan Dillon 31 Mar '09

31 Mar '09

Dear FreeSurfers, I'm having a little trouble getting something that works in optseq to work in optseq2. Here's what' is going on . . . when I run this command, things work fine and I get 6 nice sequences: optseq -ntp 170 -TR 3 -npercond 4 4 4 4 4 4 -tpercond 17 17 17 17 17 17 -label NgReal NgLook NgPhoto NuReal NuLook NuPhoto -nsessions 6 -nruns 1 -timewindow 20 -prestim 4 -nsearch 50 -o OptseqTEST However, when I run this command (i.e., my best translation of the previous command into optseq2), I get an error saying that all my schedules are ill-conditioned and I need more scan time or fewer repetitions: optseq2 --ntp 170 --tr 3 --psdwin 0 20 1 --ev NgReal 17 4 --ev NgLook 17 4 --ev NgPhoto 17 4 --ev NuReal 17 4 --ev NuLook 17 4 --ev NuPhoto 17 4 --nsearch 100 --nkeep 6 --o Optseq2TEST Is this a substantive difference between optseq and optseq2 or did I make a mistake with my optseq2 command? Also, I'm assuming there is a reason why I should use optseq2 rather than optseq, but I don't know what it is. Can someone clue me in? Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: <mailto:dillon@wjh.harvard.edu> dillon(a)wjh.harvard.edu

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GM in ROIs
by Kelly Silva 31 Mar '09

31 Mar '09

Hello, Can I calculate GM in ROIs that I have done? How can I do that? Thanks and regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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selxavg3-sess error: matrix is singular to working precision
by Jeremy Elman 30 Mar '09

30 Mar '09

Hello all, I am trying to run a first level analysis on a subject with selxavg3-sess but keep running into the same error. The dof file is created, but that is it. Any ideas what might be causing this? Below is the error given. Thank you very much for your help, Jeremy [jelman@psych118 functional]$ selxavg3-sess -s LDR001-1 -analysis LDR-fmcsm4-rec -------------------------------------------------------------- selxavg3-sess logfile is /mtl/LDR/functional/log/selxavg3-sess-bold-LDR-fmcsm4-rec-090326144433.log -------------------------------------------------------------- ------------------------------------------- /mtl/LDR/functional/LDR001-1 Thu Mar 26 14:44:35 PDT 2009 anadir = /mtl/LDR/functional/LDR001-1/bold/LDR-fmcsm4-rec ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2008 The MathWorks, Inc. Version 7.6.0.324 (R2008a) February 10, 2008 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.55.2.6 2008/05/14 20:01:35 greve Exp $ outtop = /mtl/LDR/functional Extension format = nii UseFloat = 0 INFO: acfbins is not set, setting to 10 INFO: mask is not set, setting to brain 1 old-v-new.mat Loaded /mtl/LDR/functional/LDR001-1/bold/007/ldr_paradigm.par as a par4 file. nruns = 2 autostimdur = 1 outanadir = /mtl/LDR/functional/LDR001-1/bold/LDR-fmcsm4-rec Found 155793/475136 (32.8) voxels in mask Creating Design Matrix Loaded /mtl/LDR/functional/LDR001-1/bold/007/ldr_paradigm.par as a par4 file. Warning: Matrix is singular to working precision. > In fast_selxavg3 at 208 Loaded /mtl/LDR/functional/LDR001-1/bold/011/ldr_paradigm.par as a par4 file. Warning: Matrix is singular to working precision. > In fast_selxavg3 at 208 ntptot = 364, nX = 14, DOF = 350 ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> cond at 40 s = svd(A); Error in ==> fast_selxavg3 at 239 XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n

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Freesurfer March 2009