Freesurfer April 2009

freesurfer@nmr.mgh.harvard.edu

80 participants
131 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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masking out ROIs on the surface
by Mishkin Derakhshan 07 Nov '09

07 Nov '09

Hello list, I would like to create a mask on fsaverage/surf/?h.pial that masks out the areas where the surface does not follow the cortex, but is just cutting across the mid line or across the brain stem. I know Freesurfer does this to maintain the surface toplogy, and I think it only does this in these two areas. Does a simple txt file with n vertices and a 0 or 1 value at each vertex exist somewhere? Has anyone on the list bothered to label this area manually and would be willing to share? thanks, mishkin

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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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FS-FAST mkanalysis GUI Bug. Please Read!
by Douglas N Greve 31 May '09

31 May '09

IMPORTANT! PLEASE READ! I am writing to let you know I have recently uncovered a bug in FSFAST. While I don't expect the bug to have widespread effects, the places where it does have an effect could be serious. I have set up the following web page to document the bug and help track what is being done to asses its impact and to fix it: surfer.nmr.mgh.harvard.edu/fswiki/FsFastGuiBug The bug has to do with contrasts configured with the mkanalysis Graphical User Interface (GUI). The bug is particularly bad for unbalanced contrasts, eg, comparing A to the AVERAGE of B and C. The contrast actually would compare A to the SUM of B and C. Please read the above wiki page for more details. If you have not used the GUI, then you are unaffected. I am currently developing tools to detect and fix these errors. If you are (or think you might) affected by this bug, please email me as I'd like to know exactly how widespread the problems really are. Finally, I apologize for the inconvenience that this will cause. doug ps. Thanks to Amitai Shenhav and Moshe Bar for bringing this to my attention. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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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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problem downloading freesurfer
by Dana W. Moore 05 May '09

05 May '09

I am trying to download FreeSurfer onto a different Linux machine. I am able to download, but when I try to unzip the files, I get this error message: gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now I have tried downloading it repeatedly with the same outcome. Do you know what the problem might be? I am downloading the <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.3.0/freesurfer-Linux…>freesurfer-Linux-centos4-stable-pub-v4.3.0-full.tar.gz file. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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mris_preproc really averages?
by Jeff Sadino 04 May '09

04 May '09

Hello, I ran mris_preproc on 56 subjects and then graphed the concatenated image. I also read this image into matlab and did the averaging using matlab, and then graphed the resulting image. When I did this, the two average pictures were slightly different. I thought that mris_preproc just simply averages all the subjects into common space. I noticed that its vector in matlab keeps the thickness value for all vertex's for all 56 subjects. I want to have the matlab capability for some custom processing I am doing, but the discrepancy leads me to think that mris_preproc is not a simple average. Can anyone elucidate this for me? Thank you! Matlab script. Only place I would suspect a wrong assumption is when I throw out the rest of the subjects at curv4=curv3(1,:,:,1) %Select your input thickness file path='/mnt/users/Jeff/fs/lc/HIV/pass2pics/416/diff/nc.rh.ave.mgh'; %Read the thickness file curv=MRIread(path); %Select the volume attribute curv2=curv.vol; %Create a duplicate thickness array for manipulation curv3=curv2; %Get the number of concatanated subjects tmp=size(curv2); m=tmp(4) clear 'tmp' %Sum each vertex for all your subjects for im=2:m for in=1:7 curv3(1,:,in,1)=curv3(1,:,in,1)+curv2(1,:,in,im); end end %Select just the first frame curv4=curv3(1,:,:,1); %Compute the average thickness curv.vol=curv4/m; %Write to thickness file MRIwrite(curv,'nc.rh.ave1.tmp.mgh'); _________________________________________________________________ Rediscover Hotmail®: Get quick friend updates right in your inbox. http://windowslive.com/RediscoverHotmail?ocid=TXT_TAGLM_WL_HM_Rediscover_Up…

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unsubscribe
by Bird, Anne 30 Apr '09

30 Apr '09

Please unsubscribe me from the list. Thanks! ______________________________________________ Anne C. Bird, M.S. Clinical Research Coordinator Memory and Aging Center 350 Parnassus Avenue Suite 905 University of California-San Francisco San Francisco, California 94143 Telephone: 415-476-2918 Email: abird(a)memory.ucsf.edu Website: http://memory.ucsf.edu On YouTube: www.youtube.com/ucsfmemoryandaging

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selxavg3-sess failure on analysis created with -fsv3 flag
by Jesse Friedman 30 Apr '09

30 Apr '09

Hi, I created an analysis using the -fsv3 flag and created a contrast: <mkanalysis-sess -analysis newEMerror_fsv3_std -TR 2 -paradigm error.par -designtype event-related -funcstem f0mcsm8 -tpef tpx.skip8.dat -nconditions 4 -timewindow 24 -prestim 4 -noautostimdur -fsv3> <mkcontrast-sess -contrast AScvfix -analysis newEMerror_fsv3_std -ncond 4 -wcond 0 1 0 0> and then ran selxavg3-sess: <selxavg3-sess -analysis newEMerror_fsv3_std -sf Subject_files/controlsVasd_jf.txt> which failed and gave me this error: <Computing ErrCovMtx ??? Undefined function or method 'fast_ecvm2wmtx' for input arguments of type 'double'. Error in ==> fast_selxavg3 at 492 [fsv3W fsv3AutoCor] = fast_ecvm2wmtx(ErrCovMtx);> Is this a bug, or is it that I shouldn't expect selxavg3 to work with an -fsv3 analysis in stable4? The -fsv3 flag was available in stabl4, so I gathered this meant I would be able to run selxavg3-sess in stable4. My bugr information is below. Thanks, Jesse FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.3.0-20090430 RedHat release: CentOS release 4.7 (Final) Kernel info: Linux 2.6.9-78.0.13.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: vantz SUBJECTS_DIR: /space/ventzl/16/users PWD: /space/ventzl/16/users ssh vantz setenv SUBJECTS_DIR /space/ventzl/16/users cd /space/ventzl/16/users

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Freesurfer April 2009