Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

error loading averaged brain in QDEC
by Ilana Hairston 08 Oct '10

08 Oct '10

Hi there, i ran "make_average_subject", and then tried to load the averaged brain to QDEC 1.4. I get this error message: ERROR: MRISread: file '/usr/local/FS5/subjects/avgsubject/surf/lh.avg_thickness' has many more faces than vertices! Probably trying to use a scalar data file as a surface! What am i missing? Note - the data was originally processed using FS version 4.5. thanks ilana -- ******************************* Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Sentimental Insomnia and Nostalgia Disorders Sciences ********************

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motion correction and registration of fMRI data with only one resampling
by Imri Sofer 08 Oct '10

08 Oct '10

Hello, please correct me if I am wrong, but when one processes fMRI data he usually does two spatial processing that required resampling. First he resamples the functional volume to correct for motion, and then he takes the resampled volume and resample it again to register it to the anatomical scan. I'm interested in doing these steps but with only one resampling, to minimize interpolation errors. is there any way to do it with freesurfer? thanks Imri Sofer

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Lab Coordinator Position Available
by Anthony Dick 08 Oct '10

08 Oct '10

*_Lab Coordinator Position Available_* Project on Language and Spatial Development (PLSD) and Developmental Cognitive Neuroscience (DCN) Laboratory, Florida International University (Miami, FL) *_Job Description:_* The Project on Language and Spatial Development (directed by Dr. Shannon Pruden) and the Developmental Cognitive Neuroscience Laboratory (directed by Dr. Anthony Dick) at Florida International University needs a highly capable, organized, and well-spoken individual to serve as a full-time laboratory coordinator for both labs. We seek a recent college graduate who has majored in psychology, cognitive science or neuroscience, and who is looking for additional research experience before going on to graduate school. Both labs are very active and highly collaborative with a focus on language acquisition, executive function and cognitive development in children from ages 7 months to 12 years. Applicants must be excellent with young children and their parents, and must be able to supervise undergraduate research assistants. Primary duties will include managing all aspects of the research, including behavioral, eye-tracking, and neuroimaging (fMRI) studies. *_Primary Responsibilities:_* · Maintaining participant database. · Managing participant recruitment and participant scheduling. · Overseeing lab organization, including the supervision and training of research assistants. · Conducting research activities, including the development of experimental protocols, submission of IRB forms, and data collection, coding and analysis. · Additional administrative duties include requisition of new equipment and materials, and hardware/software maintenance *_Required Experience_* · Must have a four-year Bachelors degree or equivalent in a science, educational, or technical-related field. · Must have at least two (2) years of experience working with infants or young children. · Must be proficient with the following applications: Microsoft Office (Word, Excel, Powerpoint); SPSS or equivalent statistical package; Filemaker Pro or equivalent database software. · Excellent writing skills are essential as additional duties include writing grant reports, conducting literature reviews, and collaborating on manuscripts and conference abstracts and presentations. *_Preferred Experience_* The following experiences are a plus but are not required:? · Bilingual English/Spanish speaker preferred. · Proficiency with video editing software including: Final Cut Pro or equivalent · Experience with eye-tracking technology and data analysis. · Experience with fMRI technology and data analysis. · Experience with language coding methods & software, including ELAN and/or Supercoder. ?? This job offers competitive salary (commensurate with experience), health benefits, and a dynamic work environment where laboratory coordinators are treated as colleagues. Position to begin as early as January 2011 and renewable for up to 2 years (possibly 3, contingent on available funding). A verbal two-year commitment is required. Florida International University is a vibrant, student-centered public research university, ideally located in Miami, that is worlds ahead in its commitment to learning, research, entrepreneurship, innovation, and creativity. To apply for this position, please submit a curriculum vita or resume, cover letter, and two letters of recommendation to Dr. Shannon Pruden at shannon.pruden(a)fiu.edu <mailto:shannon.pruden@fiu.edu> or Dr. Anthony Dick at anthony.dick(a)fiu.edu <mailto:anthony.dick@fiu.edu>. FIU is an EO/EA/AA employer. -- Anthony Steven Dick, Ph.D. Assistant Professor Department of Psychology Florida International University Modesto A. Maidique Campus DM 296B 11200 S.W. 8th Street Miami, FL 33199 Phone: 305-348-4202 Fax: 305-348-3879 Email: adick(a)fiu.edu Webpage: http://www.fiu.edu/~adick

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multiecho MPRAGE (MEMPR)
by Deniz Ozgen 08 Oct '10

08 Oct '10

Hello All: I read the paper by Kouwe et al. (2008 NeuroImage 40 p.559). I was wondering if FreeSurfer (v4.5) is able utilize the multi echo (especially T2-SPACE) sequence in order achieve better segmentation of GM from dura. The paper mentions the code was altered to do this. If it is possible, is there an additional option or is it able to it by default? I searched the email archive but I couldn't find much information on this topic. Thanks in advance. Deniz Ozgen.

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Re: [Freesurfer] spmregister error
by Chindhuri Selvadurai 07 Oct '10

07 Oct '10

Hello, Changing the spm path to spm5 did not fix the problem. Command line: bbregister --s RMCON051 --mov ../bold/009/f.nii --reg ../bold/register.dat --init-spm --bold Scripts directory: /space/ventzl/36/users/RespMon12C/scripts SUBJECTS_DIR: /space/ventzl/36/users/RespMon12C/subjects terminal output: vantz:chinsel[102] nmrenv -------- freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable4 FSFAST_HOME /usr/local/freesurfer/stable4/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /space/ventzl/36/users/RespMon12C/subjects MNI_DIR /usr/local/freesurfer/stable4/mni FSL_DIR /usr/pubsw/packages/fsl/current [vantz:scripts] (nmr-std-env) pwd /autofs/space/ventzl_036/users/RespMon12C/scripts [vantz:scripts] (nmr-std-env) ./ bbregister.bash ./: Permission denied. [vantz:scripts] (nmr-std-env) ./bbregister.bash Log file is ../bold/register.dat.log Thu Oct 7 10:07:04 EDT 2010 setenv SUBJECTS_DIR /space/ventzl/36/users/RespMon12C/subjects cd /autofs/space/ventzl_036/users/RespMon12C/subjects/RMCON051/mystudy /usr/local/freesurfer/stable4/bin/bbregister --s RMCON051 --mov ../bold/009/f.nii --reg ../bold/register.dat --init-spm --bold $Id: bbregister,v 1.14.2.13 2009/12/16 20:20:09 greve Exp $ Linux vantz 2.6.18-194.8.1.el5 #1 SMP Thu Jul 1 19:04:48 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/stable4 mri_convert ../bold/009/f.nii ../bold/tmp.bbregister.26962/template.nii mri_convert ../bold/009/f.nii ../bold/tmp.bbregister.26962/template.nii $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from ../bold/009/f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997195, -0.0748521, -0.000274916) j_ras = (0.0748328, -0.997009, 0.0193167) k_ras = (-0.00171999, 0.0192419, 0.999813) writing to ../bold/tmp.bbregister.26962/template.nii... spmregister --s RMCON051 --mov ../bold/tmp.bbregister.26962/template.nii --reg ../bold/tmp.bbregister.26962/reg.init.dat --tmp ../bold/tmp.bbregister.26962/spmregister Log file is ../bold/tmp.bbregister.26962/spmregister.log Thu Oct 7 10:07:14 EDT 2010 --s RMCON051 --mov ../bold/tmp.bbregister.26962/template.nii --reg ../bold/tmp.bbregister.26962/reg.init.dat --tmp ../bold/tmp.bbregister.26962/spmregister $Id: spmregister,v 1.21.2.5 2009/04/15 18:10:23 greve Exp $ matlab matlab fmt img UseSPMGetSpace 1 -------------------------------------- /autofs/space/ventzl_036/users/RespMon12C/subjects/RMCON051/mystudy mri_convert /space/ventzl/36/users/RespMon12C/subjects/RMCON051/mri/brainmask.mgz ../bold/tmp.bbregister.26962/spmregister/refvol.spmregister.img -ic 0 0 0 mri_convert /space/ventzl/36/users/RespMon12C/subjects/RMCON051/mri/brainmask.mgz ../bold/tmp.bbregister.26962/spmregister/refvol.spmregister.img -ic 0 0 0 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /space/ventzl/36/users/RespMon12C/subjects/RMCON051/mri/brainmask.mgz... TR=2530.00, TE=1.64, TI=1200.00, flip angle=7.00 i_ras = (-1, -1.49012e-08, -2.12167e-08) j_ras = (-9.8953e-08, -7.69251e-09, -1) k_ras = (3.72529e-08, 1, 4.14548e-09) writing to ../bold/tmp.bbregister.26962/spmregister/refvol.spmregister.img... Analyze Output Matrix -1.000 -0.000 0.000 129.000; -0.000 -0.000 1.000 -129.000; -0.000 -1.000 0.000 129.000; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 -------------------------------------- /autofs/space/ventzl_036/users/RespMon12C/subjects/RMCON051/mystudy mri_convert ../bold/tmp.bbregister.26962/template.nii ../bold/tmp.bbregister.26962/spmregister/movvol.spmregister.img -ic 0 0 0 --frame 0 mri_convert ../bold/tmp.bbregister.26962/template.nii ../bold/tmp.bbregister.26962/spmregister/movvol.spmregister.img -ic 0 0 0 --frame 0 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from ../bold/tmp.bbregister.26962/template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997195, -0.0748521, -0.000274916) j_ras = (0.0748328, -0.997009, 0.0193167) k_ras = (-0.00171999, 0.0192419, 0.999813) keeping frame 0 writing to ../bold/tmp.bbregister.26962/spmregister/movvol.spmregister.img... Analyze Output Matrix -3.116 0.234 -0.006 95.227; -0.234 -3.116 0.071 109.325; -0.001 0.060 3.699 -64.852; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 Matlab file is ../bold/tmp.bbregister.26962/spmregister/spmregister.27005.m monly = 0; targvol = '../bold/tmp.bbregister.26962/spmregister/refvol.spmregister.img'; srcvol = '../bold/tmp.bbregister.26962/spmregister/movvol.spmregister.img'; errfile = '../bold/tmp.bbregister.26962/spmregister/spmregister.27005.err'; if(exist('spm_coreg') ~= 2) fprintf('ERROR: cannot find spm_coreg.m. Make sure that the SPM\n'); fprintf(' package is in your matlab path (check ~/matlab/startup)\n'); fp = fopen(errfile,'w'); fprintf(fp,'ERROR: cannot find spm_coreg.m. Make sure that the SPM\n'); fprintf(fp,' package is in your matlab path (check ~/matlab/startup)\n'); fclose(fp); return; quit; end which spm_coreg global defaults spm_defaults % load spm2's default fields fprintf('INFO: Assuming RAS coordinate system\n'); defaults.analyze.flip = 0; %=========================================================================== % coregistration defaults %=========================================================================== defaults.coreg.estimate.cost_fun = 'nmi'; defaults.coreg.estimate.sep = [4 2]; defaults.coreg.estimate.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001]; defaults.coreg.estimate.fwhm = [7 7]; defaults.coreg.estimate.params = [0 0 0 0 0 0]; defaults.coreg.estimate.graphics = 0; % dont crate ps file %=========================================================================== % coregister files %=========================================================================== disp(sprintf('using %s as the target image',targvol)); disp(sprintf('using %s as the source image',srcvol)); [pth1,nam1,ext1] = fileparts(deblank(targvol)); [pth2,nam2,ext2] = fileparts(deblank(srcvol)); %tmp = spm_get('Files',pth1,[nam1 ext1]); tmp = sprintf('%s/%s%s',pth1,nam1,ext1); VG = spm_vol(tmp); % target image if(isempty(VG)) fprintf('ERROR: loading target %s\n',targvol); fp = fopen(errfile,'a'); fprintf(fp,'ERROR: loading target %s\n',targvol); fclose(fp); return; quit; end % tmp = spm_get('Files',pth2,[nam2 ext2]) tmp = sprintf('%s/%s%s',pth2,nam2,ext2); VF = spm_vol(tmp); % source image if(isempty(VF)) fprintf('ERROR: loading source %s\n',srcvol); fp = fopen(errfile,'a'); fprintf(fp,'ERROR: loading source %s\n',srcvol); fclose(fp); return; quit; end fprintf('\n\nINFO: ignore warnings about scalefactor\n\n'); disp('determining coregistration parameters...') tic; try x = spm_coreg(VG.fname,VF.fname,defaults.coreg.estimate); catch fprintf('ERROR: spm_coreg\n'); fp = fopen(errfile,'a'); fprintf(fp,'ERROR: spm_coreg\n'); fprintf(fp,'%s\n',which('spm_coreg')); fclose(fp); return; quit; end if(isempty(x)) fprintf('ERROR: spm_coreg\n'); if(~monly) fp = fopen(errfile,'a'); fprintf(fp,'ERROR: spm_coreg\n'); fclose(fp); return; quit; end end fprintf('Finished after %g sec\n',toc); fprintf('Parameters '); fprintf('%g ',x); fprintf('\n'); %---------write out the .mat file---see spm_coreg_ui.m line 283 M = inv(spm_matrix(x)); if(1) fprintf('Using spm_get_space\n'); MM = zeros(4,4,1); MM = spm_get_space(deblank(VF.fname)); spm_get_space(deblank(VF.fname), M*MM); fprintf('\n\nINFO: ignore warnings about scalefactor\n\n'); else fprintf('Using MRIread/write instead of spm_get_space\n'); ff = MRIread(deblank(VF.fname)); ff.vox2ras1 = M*ff.vox2ras1; ff.vox2ras0 = vox2ras_1to0(ff.vox2ras1); ff.vox2ras = ff.vox2ras0; MRIwrite(ff,deblank(VF.fname)); end return; if(~monly) quit; end Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen. Warning: No window system found. Java option 'MWT' ignored < M A T L A B > Copyright 1984-2007 The MathWorks, Inc. Version 7.4.0.287 (R2007a) January 29, 2007 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. Warning: Executing startup failed in matlabrc. This indicates a potentially serious problem in your MATLAB setup, which should be resolved as soon as possible. Error detected was: MATLAB:UndefinedFunction Undefined function or variable 'mne_setup_toolbox'. > In matlabrc at 259 >> >> >> >> >> >> >> ERROR: cannot find spm_coreg.m. Make sure that the SPM package is in your matlab path (check ~/matlab/startup) >> >> 'spm_coreg' not found. >> >> >> ??? Undefined function or variable 'spm_defaults'. >> >> INFO: Assuming RAS coordinate system >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> using ../bold/tmp.bbregister.26962/spmregister/refvol.spmregister.img as the target image >> using ../bold/tmp.bbregister.26962/spmregister/movvol.spmregister.img as the source image >> >> >> >> >> >> >> ??? Undefined function or method 'spm_vol' for input arguments of type 'char'. >> ??? Undefined function or variable 'VG'. >> >> >> ??? Undefined function or method 'spm_vol' for input arguments of type 'char'. >> ??? Undefined function or variable 'VF'. >> >> INFO: ignore warnings about scalefactor >> >> determining coregistration parameters... >> >> >> ERROR: spm_coreg >> ??? Undefined function or variable 'x'. >> Finished after 0.008886 sec >> >> Parameters >> ??? Undefined function or variable 'x'. >> >> >> >> >> ??? Undefined function or variable 'x'. >> >> Using spm_get_space ??? Undefined variable "VF" or class "VF.fname". >> >> >> ERROR: matlab exited with errors ERROR: cannot find spm_coreg.m. Make sure that the SPM package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg > Two suggestions: > 1. Can you temporarily change the spm path to spm5 to see if that fixes the problem? > 2. Can you send me your command line, directory you ran it from, SUBJECTS_DIR, and terminal output? > doug > Chindhuri Selvadurai wrote: >> The path to spm2 was not originally in my startup.m file, but even when I added it, it didn't work. >> I am using 7.8, but I tried to change my cshrc file back to 7.1 however, >> once I ran the script, it was actually running 7.4 >> Thank you, >> Chindhuri >>> Chindhuri, >>> Is the path to spm2 added in your startup.m file and are you using >> matlab 7.1 (required by spm2)? >>> doug >>> Chindhuri Selvadurai wrote: >>>> Hello, >>>> I am getting the same error that was discussed in the attached thread, >> however, the addition of the path line did not work for me. >>>> I am also not sure if we should be using spm5 since all in the past we >> have been using spm2. It presents this error when running under my name, >>>> but not for other users. >>>> Any help would be appreciated! >>>> Thanks, >>>> Chindhuri >>>> ________________________________________________ >>>> Re: [Freesurfer] spmregister error >>>> Douglas N Greve >>>> Fri, 30 Jul 2010 09:58:18 -0700 >>>> Yes, that should work. >>>> doug >>>> Adam Nitenson wrote: >>>>> Hi Sandra, >>>>> I just had this same problem about a week ago. The solution which >>>>> worked for me was adding the following line of text into the startup.m >> file in your matlab folder: >>>>> path(path,'/usr/pubsw/common/spm/spm5'); >>>>> I'm not sure it matter exactly where you put it. I put mine in the >> last >>>>> row in the FreeSurfer FAST section, under the line beginning with >> "clear". >>>>> Hope that helps! >>>>> -Adam >>>>>> Hello, >>>>>> When running spmregister-sess (standard environment was sourced) I >> encountered this error: >>>>>> ERROR: matlab exited with errors >>>>>> ERROR: cannot find spm_coreg.m. Make sure that the SPM >>>>>> package is in your matlab path (check ~/matlab/startup) >>>>>> ERROR: spm_coreg >>>>>> ERROR: spmregister failed >>>>>> __________________________________________________________ >>>>>> Our information: >>>>>> FREESURFER_HOME: /usr/local/freesurfer/stable4 >>>>>> Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 >> RedHat release: CentOS release 5.3 (Final) >>>>>> Kernel info: Linux 2.6.18-128.7.1.el5 x86_64 >>>>>> NMR Center info (/space/freesurfer exists): >>>>>> machine: purkinje >>>>>> SUBJECTS_DIR: /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons >>>>>> PWD: /cluster/ablood/1/DMRF_ASL >>>>>> ssh purkinje >>>>>> setenv SUBJECTS_DIR /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons cd >> /cluster/ablood/1/DMRF_ASL >>>>>> __________________________________________________________________ We >> appreciate any help you can give us!! >>>>>> Thanks, >>>>>> Sandra >>>>>> Mood and Motor Control Laboratory >>>>>> Athinoula Martinos Center for Biomedical Imaging >>>>>> Massachusetts General Hospital >>>>>> 120 6th St. >>>>>> Charlestown, MA 02129 >>>>>> Tel: 617-643-6245 >>>>>> Fax: 617-726-1351 >>>>>> Email: swoodm...(a)partners.org >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> Adam Nitenson, B.S. >>>>> Brain Genomics Lab >>>>> Massachusetts General Hospital >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Best, >> Chindhuri Selvadurai >> Psychiatric Neuroimaging, Manoach Lab >> Martinos Center for Biomedical Imaging >> Massachusetts General Hospital >> Phone: (617)726-0307 > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging Massachusetts General Hospital Phone: (617)726-0307 Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging Massachusetts General Hospital Phone: (617)726-0307

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FSL-VBM help
by Alan Francis 07 Oct '10

07 Oct '10

Hi All: This is for the FSL VBM experts out there. I have finished all the pre processing steps for a dataset using FSL VBM and I am trying to design a matrix for statistical analysis. I am having difficulty with the *design.mat * file and the* design.con* files. Do any of you know an easy of creating this so that it can perform GLM stats on my data? I tried FEAT but it works best only for fMRI. thanks, Alan

1 0

selxavg3 problems - missing mcextreg files
by Adam Nitenson 07 Oct '10

07 Oct '10

Hi all, I'm having an issue with selxavg3-sess in Stable 4. I've run all commands up to this point without error. Here was the command I used selxavg3-sess -s FB0011099AA -analysis fmcsm5_functionals and the error: ERROR: cannot find volume matching /autofs/cluster/roffman/users/folate_subjects/FB0011099AA/bold/015/mcextreg ERROR: loading nonpar reg /autofs/cluster/roffman/users/folate_subjects/FB0011099AA/bold/015/mcextreg >From looking at the other bold folders...it's clear that I'm missing the "mcextreg" files in /cluster/roffman/users/folate_subjects/FB0011099AA/bold/015 which seems to halt the command What is the best way to recover these files for this one BOLD folder? Thanks, Adam Nitenson PS Here is the additional computer info: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.5.0-20100311 RedHat release: CentOS release 5.5 (Final) Kernel info: Linux 2.6.18-194.8.1.el5 i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /cluster/roffman/users/folate_subjects PWD: /cluster/roffman/users/folate_subjects ssh seymour setenv SUBJECTS_DIR /cluster/roffman/users/folate_subjects cd /cluster/roffman/users/folate_subjects

3 2

zero cortical thickness in the lingual and precuneus
by Wang, Xin 07 Oct '10

07 Oct '10

Hello, Dr. Fischl, I asked this quesion about zero thickness in the sulcus next to the lateral vertricle before, and corrected the wrong label of lateral vertricle in the aseg.mgz file and added white matter between lateral vertricle and this sulcus in the wm.mgz. But the problem is still exist in some slices after multiple times of correction. We have this problem in version 4.4.X to 4.5.0. My questions are 1) Do you have any additional suggestion to fix this bug? 2) If not, do you have a way to exclude this problematic sulcus? In another word, can we include this sulcus in the unknown zone? I don't like to exclude entire lingual, precunneus, and pericalcarine regions from mean thickness analysis and vertex-based analysis because these three labels occupy a large part of cortex. Thank you in advance, Xin Wang ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of freesurfer-request(a)nmr.mgh.harvard.edu Sent: Thu 10/7/2010 11:31 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 80, Issue 12 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."

4 9

memory needed to run a freesurfer stream
by Nathan Dankner 07 Oct '10

07 Oct '10

Hi all, I was curious as to approximately how much memory is required to run a surface through autorecon 1 and 2, and autorecon 2 and 3. I'm running them on a new server where I have to request resources, so a ballpark figure is really all I need. Thanks! Nathan

4 3

Defining cluster threshold
by Jacobs H (NP) 07 Oct '10

07 Oct '10

Hi FreeSurfers, I have done my DTI analyses (dt_recon with TBSS) and the statistical analyses in FreeSurfer. Now I have defined the clustersize with mri_volcluster, but I find this rather arbitrary. Is there a way to calculate a minimum size cluster threshold (by using for example a Monte Carlo simulation)? Thanks! Heidi

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