Freesurfer March 2008

freesurfer@nmr.mgh.harvard.edu

55 participants
81 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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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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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 measures - normalised?
by Narly A Golestani 21 Jun '08

21 Jun '08

Dear all, Am I correct in thinking that the measures of cortical volume, area, and thickness, as well as subcortical volumes obtained after running the reconall pipeline (and found in the 'aparc' and 'aseg' files, respectively) are native ones? Or are they based on normalised brains, thus 'controlling' for overall brain volume differences? thanks, Narly.

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variables and glmfit...
by Cameron Ellis 02 Apr '08

02 Apr '08

Hi all, I have two questions regarding glmfit and testing for effects of different variables. I have four groups. When testing for effects of age across all of the groups, will there be a difference when assigning each group a class in my fsgd file, with age as a variable, like so: Class PH Class PL Class VH Class VL Variables age Input NEAA004 PH 30 Input NEAA006 PH 21 Input NEAA007 PL 42 Input NEAA020 PL 27 Input NEAA024 VH 26 Input NEAA025 VH 24 Input NEAA039 VL 24 Input NEAA052 VL 33 . . etc... and setting up a contrast matrix: 0 0 0 1; and alternatively setting up my fsgd file with a single group, like so: Class subj Variables age Input NEAA004 subj 30 Input NEAA006 subj 21 Input NEAA007 subj 42 Input NEAA020 subj 27 Input NEAA024 subj 26 Input NEAA025 subj 24 Input NEAA039 subj 24 Input NEAA052 subj 33 . . etc... and setting up a contrast matrix: 0 1? Is the first options controlling for effects of group? Would I want to do this? My second question is in regards to controling for a discrete variable like gender. Should male and female be coded as dummy variables 0 and 1 in the fsgd file? I have tried this and my results seem to make more sense than when I run the same analysis in qdec where I did not code the variables in this way. Should I be doing so in qdec as well? Thanks! Cameron

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mri_surfcluster CWP values
by James N Porter 01 Apr '08

01 Apr '08

Hello- When I look at the CWP results of mri_surfcluster in the sig.cluster.sum versus the resultant sig.cluster.mgh, the results are different. Specifically, all clusters negatively correlated with my independent variable display a value in tksurfer of -1+CWP, and clusters that are positively correlated display a value of 1-CWP. Which values should I believe as my actual p-values, the .sum's CWP or the .mgh's added/subtracted values? Thanks for your help, --------- Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota

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glm_fit question...
by Cameron Ellis 01 Apr '08

01 Apr '08

Hi all, Is it necessary to include a value in your contrast matrix for every class and variable in your fsgd file? It seems that this is the case. My understanding is that if you weight a variable 0 then it is automatically controlled for. So if am required to weight a variabe in the contrast matrix that do not want to control for, then to not control for it I have to make a different fsgd file without that variable? Thanks, Cameron

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error while loading shared libraries:libtiff.so.3
by Lúcia Garrido 30 Mar '08

30 Mar '08

Hello, I'm using Debian and downloaded freesurfer-Linux-centos4-stable-pub-v4.0.2-full.tar.gz. Everything worked fine when I tested the installation with tkmedit and tksurfer. I then ran recon-all -i C04_SS.nii -autorecon1 -s C04_SS and it also finished without errors. But when I ran recon-all -autorecon2 -s C04_SS, there was an error at the end saying: mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory I've checked the shared libraries and I have libtiff.so.4. Could you let me know how to get libtiff.so.3 to work and if I should do something else? Thank you very much. Lucia

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[Fwd: Re: [Freesurfer] Error]
by jake＠nmr.mgh.harvard.edu 28 Mar '08

28 Mar '08

Hi, Thanks for the bugr command. Here is my information, Thank you! Please include the following additional information in your report: 1) subject name: CD_aftbotox_ctrl5 2) the entire command-line executed csh CD_aftbotox_ctrl5_ContrastAnalysis.csh 3) the error message generated (please see below, our preprocessing step is built into our csh file.) 4) optionally include the subject's /script/recon-all.log **The logfile for preprocessing can be found in: > /autofs/space/meso_018/users/ablood/cerv/log > striatum:jake[107] more preproc-CD_aftbotox_ctrl5-bold.log --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable3 Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070717 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-8.1.15.el5 i686 NMR Center info (/space/freesurfer exists): machine: striatum SUBJECTS_DIR: /space/sake/3/users/inverse/subjects ***(this is set to be /space/meso/18/users/ablood/cerv by the .csh script) PWD: /homes/14/jake/AnalysisPrograms --------------------------------------------------------------------- ---------------------------- Original Message ---------------------------- Subject: Re: [Freesurfer] Error From: "Pratap Kunwar" <pkunwar(a)nmr.mgh.harvard.edu> Date: Fri, March 28, 2008 12:00 pm To: jake(a)nmr.mgh.harvard.edu -------------------------------------------------------------------------- Jake, Are you doing preprocessing or stxgrinder, and are you running from > *running from the following directory > /autofs/homes/014/jake/AnalysisPrograms or /autofs/space/meso_018/users/ablood/cerv/ ? it will be nice if you provide more info. use "bugr" to get report and send to freesurfer. about bugreporting, https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting?action=highlight&val… pratap > Hi, > > We are getting an error where our preprocessing step seems to be failing, > any help would be greatly appreciated, thank you! > > > > *using the following command (which sources > /usr/local/freesurfer/nmr-stable3-env) > striatum:jake[85] csh CD_aftbotox_ctrl5_ContrastAnalysis.csh > > *error: > --- Parsing Config File: > /autofs/space/meso_018/users/ablood/cerv/tap_rh_short_CD_aftbotox_ctrl5_sm4/analysis.cfg > ---- > -gammafit 2.25 1.25 -timewindow 25.0000 -prestim 0 -polyfit 1 -TER 2.5000 > -nskip 0 -fwhm 0 -rescale 1000 > ERROR: 022/fmcsm4 does not have a .meanval file, run inorm > ERROR (/autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5): > selxavg failed > ERROR: cannot find tap_rh_short_CD_aftbotox_ctrl5_sm4/h.dat > -------------------------------------------------------------- > stxgrinder-sess logfile is > /autofs/space/meso_018/users/ablood/cerv/log/stxgrinder-sess.080328112804.log > -------------------------------------------------------------- > ERROR: analysis tap_rh_short_CD_aftbotox_ctrl5_sm4 does not exist for > /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5 > > > > > > > > **The logfile for preprocessing can be found in: > /autofs/space/meso_018/users/ablood/cerv/log > striatum:jake[107] more preproc-CD_aftbotox_ctrl5-bold.log > > ***Here is the error from the logfile: > to3d WARNING: > Significant outliers detected in these sub-bricks: > 60 103 104 105 106 107 108 120 122 > You should inspect the dataset for possible corruption. > [Outliers are defined as in program 3dToutcount. ] > [Outliers early in an EPI time series may be due to ] > [the longitudinal magnetization equilibration effect.] > [Other causes are subject movement, scanner problems,] > [or anything that makes a time series look irregular.] > [ 3dToutcount -save outnam dataset | 1dplot -stdin ] > [can be used to make a dataset 'outnam' that marks ] > [outlier voxels; see 3dToutcount -help for details. ] > > ++ 3D dataset written to disk > -------------- Motion Correcting --------------------------- > /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5/bold/mctmp > set VR = 3dvolreg > 3dvolreg -verbose -dfile > /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ct > rl5/bold/018/fmc4.mcdat -prefix 6776.volreg -base targ-6776+orig[0] > 6776+orig > ++ Program 3dvolreg: AFNI version=AFNI_2006_03_21_1314 [32-bit] > ++ Authored by: RW Cox > ++ Reading in base dataset ./targ-6776+orig.BRIK > ** Input ./6776+orig.HEAD and base ./targ-6776+orig.HEAD don't have same > dimensi > ons! > Input: nx=64 ny=64 nz=30 > Base: nx=64 ny=64 nz=16 > ** FATAL ERROR: perhaps you could make your datasets match? > set st = 1 > if ( 1 ) then > echo ERROR: 3dvolreg existed with status 1 > ERROR: 3dvolreg existed with status 1 > exit 1 > ERROR: mc-sess failed > > > > > Thanks, > > Jake > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Error
by jake＠nmr.mgh.harvard.edu 28 Mar '08

28 Mar '08

Hi, We are getting an error where our preprocessing step seems to be failing, any help would be greatly appreciated, thank you! *running from the following directory /autofs/homes/014/jake/AnalysisPrograms *using the following command (which sources /usr/local/freesurfer/nmr-stable3-env) striatum:jake[85] csh CD_aftbotox_ctrl5_ContrastAnalysis.csh *error: --- Parsing Config File: /autofs/space/meso_018/users/ablood/cerv/tap_rh_short_CD_aftbotox_ctrl5_sm4/analysis.cfg ---- -gammafit 2.25 1.25 -timewindow 25.0000 -prestim 0 -polyfit 1 -TER 2.5000 -nskip 0 -fwhm 0 -rescale 1000 ERROR: 022/fmcsm4 does not have a .meanval file, run inorm ERROR (/autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5): selxavg failed ERROR: cannot find tap_rh_short_CD_aftbotox_ctrl5_sm4/h.dat -------------------------------------------------------------- stxgrinder-sess logfile is /autofs/space/meso_018/users/ablood/cerv/log/stxgrinder-sess.080328112804.log -------------------------------------------------------------- ERROR: analysis tap_rh_short_CD_aftbotox_ctrl5_sm4 does not exist for /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5 **The logfile for preprocessing can be found in: /autofs/space/meso_018/users/ablood/cerv/log striatum:jake[107] more preproc-CD_aftbotox_ctrl5-bold.log ***Here is the error from the logfile: to3d WARNING: Significant outliers detected in these sub-bricks: 60 103 104 105 106 107 108 120 122 You should inspect the dataset for possible corruption. [Outliers are defined as in program 3dToutcount. ] [Outliers early in an EPI time series may be due to ] [the longitudinal magnetization equilibration effect.] [Other causes are subject movement, scanner problems,] [or anything that makes a time series look irregular.] [ 3dToutcount -save outnam dataset | 1dplot -stdin ] [can be used to make a dataset 'outnam' that marks ] [outlier voxels; see 3dToutcount -help for details. ] ++ 3D dataset written to disk -------------- Motion Correcting --------------------------- /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5/bold/mctmp set VR = 3dvolreg 3dvolreg -verbose -dfile /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ct rl5/bold/018/fmc4.mcdat -prefix 6776.volreg -base targ-6776+orig[0] 6776+orig ++ Program 3dvolreg: AFNI version=AFNI_2006_03_21_1314 [32-bit] ++ Authored by: RW Cox ++ Reading in base dataset ./targ-6776+orig.BRIK ** Input ./6776+orig.HEAD and base ./targ-6776+orig.HEAD don't have same dimensi ons! Input: nx=64 ny=64 nz=30 Base: nx=64 ny=64 nz=16 ** FATAL ERROR: perhaps you could make your datasets match? set st = 1 if ( 1 ) then echo ERROR: 3dvolreg existed with status 1 ERROR: 3dvolreg existed with status 1 exit 1 ERROR: mc-sess failed Thanks, Jake

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Freesurfer March 2008