Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

FW: Extracting coordinates of segmented volume
by Eggebrecht, Adam 08 Oct '10

08 Oct '10

Hello there, I am just getting started with learning the ways of FreeSurfer. I am hoping you can help explain how (and if) FreeSurfer can give me the information I need. I want to use FS's segmentation to better label optical properties in the head for optical reconstructions. Does FS output the coordinates and labels for the segmented volume (gray matter, white matter, csf)? Also good would be the affine transform so it can be inverted to put the coordinates of the segmented and labelled nodes (voxels?) back into native space. I am performing our head segmentation and optical analysis in MATLAB. Any help supplied is greatly appreciated. Many thanks! Adam Adam T. Eggebrecht, Ph.D. Dept. of Radiology Washington University School of Medicine St. Louis, MO 314-362-6942 The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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mri_convert with flash - FS 4.5.0 vs 5.0
by Ellen Lau 08 Oct '10

08 Oct '10

Hi, We're having trouble using mri_convert as wrapped within mne_flash_bem to create the bem surfaces from our FLASH volumes. The script runs but the inner_skull and outer_skull surfaces that it outputs seem to be rotated, for example if we display the surfaces on the T1 coronal, we see what looks like the sagittal inner_skull surface. I'm guessing this is some kind of registration problem. I noticed that we are getting a warning at one point in the process when the flash is being registered with the MPRAGE, which I've pasted below. I am wondering if this might have something to do with the switch to version 5.0.0. For this dataset, we ran the reconstruction and all the subsequent processing on v5.0.0. However, I have gotten the exact same error (rotated inner and outer skull surfaces) when I accidentally ran mne_flash_bem in v5.0 with a previous dataset that was reconstructed in v4.5.0. When I re-ran mne_flash_bem in v4.5.0 the surfaces came out correctly for the previous dataset. But I was reluctant to try this with my new dataset since ideally we'd like to be able to switch completely over to v5.0.0. Thanks, Ellen --------------- [kerryave:test] (nmr-std-env) which mri_convert /usr/local/freesurfer/stable5/bin/mri_convert setenv SUBJECTS_DIR /cluster/kuperberg/SemPrMM/MRI/structurals/subjects/ selected output from mne_flash_bem containing the warning: /autofs/cluster/kuperberg/SemPrMM/MRI/structurals/subjects/ya1/mri/flash/parameter_maps mri_convert ./fsl_rigid_register.7595/outvol.fsl_rigid_register.nii flash5_reg.mgz mri_convert ./fsl_rigid_register.7595/outvol.fsl_rigid_register.nii flash5_reg.mgz $Id: mri_convert.c,v 1.166.2.4 2010/09/20 17:29:33 nicks Exp $ reading from ./fsl_rigid_register.7595/outvol.fsl_rigid_register.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 5.63785e-17) j_ras = (0, 3.67872e-08, -1) k_ras = (0, 1, -1.5134e-08) writing to flash5_reg.mgz... /autofs/cluster/kuperberg/SemPrMM/MRI/structurals/subjects/ya1/mri/flash/parameter_maps mri_copy_params flash5_reg.mgz flash5.mgz flash5_reg.mgz WARNING: volume sizes are different in_vol : 256, 256, 256 temp_vol : 256, 256, 176 Cleaning up

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error loading averaged brain in QDEC (2)
by Ilana Hairston 08 Oct '10

08 Oct '10

sorry - on further inspection i changed "Common-Space Subject" to the new averaged subject folder. However, when trying to run analyses, i get an error message: Error in Analyze: Couldn't open file /usr/local/FS5/subjects/FS080920cr/surf/lh.thickness.fwhm10.avgsubject.mgh (where"avgsubject" was the output name of the averaged subject template). Indeed, there are ?h.?.fwhm?.fsaverage.mgh in my subject folders (presumable from the previous preproc), but no new ones. 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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Creating Brainmaps for Significant Regression
by Adam Nitenson 08 Oct '10

08 Oct '10

Hi all, So far I have only been using Freesurfer analyses to look at the functional activation for individuals, single groups, and subtractions between 2 groups. We now want to investigate a possible linear relationship between allele load (Three levels: 0,1,2) and functional activation. Is there a way to create a brainmap using glmfit or some other command that displays voxels that display a significant regression of genotype (such as red for positive / blue for negative linear relationship)? Basically, it would be a map that shows significant "r" instead of significant difference. Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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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

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