Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30097 discussions

qdec question: discrepancy in sig. clusters
by Maria Kharitonova 26 Jul '13

26 Jul '13

Hello, I have another newbie question. I'm running qdec, trying to compare cortical thickness in children with and without ADHD. However, I'm seeing a discrepancy between the clusters that are significant according to the terminal (after applying the Monte-Carlo simulation with default parameters; output below) and the ones that pop up when I hit "Find clusters and goto Max". For example, I'm seeing 4 regions in the terminal: medialorbitalfrontal, inferiorparietal, caudalmiddlefrontal, and precentral. However, when I hit "Find clusters and goto Max", I only see the Frontalpole. Using mri_surfcluster to extrat thickness measures only extracts it for the frontalpole, and not for the 4 ROIs listed in the terminal. I would like to be able to extract stats on those 4 that are listed in the terminal, if possible. Can you please help me reconcile the 2 types of output? Thanks! *** terminal output: # Input /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final/qdec/dx_age_icv_nuis_lh/rh-Diff-CONTROL-ADHD-Cor-thickness-age/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi rh # surface white # annot aparc # SUBJECTS_DIR /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 4.75828 at vertex 134555 # Overall min -2.56762 at vertex 93241 # NClusters 4 # Total Cortical Surface Area 65020.8 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 4.758 134555 1015.59 8.7 58.2 -5.8 0.00010 0.00000 0.00020 1292 medialorbitofrontal 2 3.968 135840 466.91 40.0 -66.8 25.9 0.01790 0.01620 0.01960 750 inferiorparietal 3 3.954 115431 497.60 29.3 21.4 39.9 0.01150 0.01010 0.01290 900 caudalmiddlefrontal 4 3.242 133890 439.44 49.4 -5.1 22.0 0.02520 0.02320 0.02720 932 precentral Simulation complete.

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retinotopy betas
by dgw 26 Jul '13

26 Jul '13

Hi, I am examining the affect a metal artifact has on fMRI data, and I am using Eccentricity mapping with the retinotopy analysis in FSFast. I was recently asked to switch from examining the difference in the fsig to examining the difference in the betas. I opened up beta.nii.gz and I can see that it has a size of: 1 #of vertices 1 39 Can you explain to me, how I figure out where each of the 39 come from (and possibly point me to which of these might be appropriate to use?)? Thank You, Dan

3 4

functional connectivity, group averages
by Mario Ortega 26 Jul '13

26 Jul '13

Hi Team, I have a question on making a group average of subjects for functional connectivity. In detail, I want to make a surface overlay that is the average correlation (r-value) of a certain subject group. What commands would be used for this? simply isxconcat-sess? I could not find much info on the FSFAST or Functional webpages. Thanks, Mario

2 1

HypoIntense Lesions
by Fotiadis, Panagiotis 26 Jul '13

26 Jul '13

Hi FreeSurfer Community, I was wondering whether there is an automatic tool that outlines the hypointense lesions in a SWI scan. Thank you, Panos

3 12

selxavg3-sess： Matlab cannot display graphics
by Wang Zhiwei 26 Jul '13

26 Jul '13

Hi all, When I run selxavg3-sess for any analysis, the following information is always appearing. Can you please give some suggestions how to fix that? Any thoughts would be very appreciated! ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. 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 (R) > Copyright 1984-2012 The MathWorks, Inc. R2012b (8.0.0.783) 64-bit (glnxa64) August 22, 2012 No window system found. Java option 'MWT' ignored. 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 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Thanks! James

2 1

spmregister error
by Marco Loggia 26 Jul '13

26 Jul '13

Hello Doug, I am encountering the error below when running spmregister. Where do you think is the issue? Thanks! Best, Marco bash-4.1$ spmregister --mov "$file".nii --s PBR_"$subj" --reg tmp.dat --fsvol merged.lrrev Log file is ./spmregister.log Fri Jul 26 10:52:49 EDT 2013 --mov rsl_CLBP001_f1_1_3627_5427_nas_suv.nii --s PBR_CLBP001 --reg tmp.dat --fsvol merged.lrrev $Id: spmregister,v 1.39.2.1 2012/10/30 20:05:17 greve Exp $ matlab matlab fmt nii UseSPMGetSpace 1 -------------------------------------- /autofs/cluster/hookerlab/Studies/PBR/Marco/CLBP001/PET/Sum_single_frame/PET_recon_SUV/rsl_files mri_convert /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz ./tmp.spmreg.10617/refvol.spmregister.nii -ic 0 0 0 mri_convert /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz ./tmp.spmreg.10617/refvol.spmregister.nii -ic 0 0 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0414768, -0.991189, -0.125791) j_ras = (-0.0799847, 0.128789, -0.988441) k_ras = (-0.995933, 0.030936, 0.084622) writing to ./tmp.spmreg.10617/refvol.spmregister.nii... -------------------------------------- /autofs/cluster/hookerlab/Studies/PBR/Marco/CLBP001/PET/Sum_single_frame/PET_recon_SUV/rsl_files mri_convert rsl_CLBP001_f1_1_3627_5427_nas_suv.nii ./tmp.spmreg.10617/movvol.spmregister.nii -ic 0 0 0 --frame 0 mri_convert rsl_CLBP001_f1_1_3627_5427_nas_suv.nii ./tmp.spmreg.10617/movvol.spmregister.nii -ic 0 0 0 --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from rsl_CLBP001_f1_1_3627_5427_nas_suv.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, -1) keeping frame 0 writing to ./tmp.spmreg.10617/movvol.spmregister.nii... Matlab file is ./tmp.spmreg.10617/spmregister.10617.m monly = 0; targvol = './tmp.spmreg.10617/refvol.spmregister.nii'; srcvol = './tmp.spmreg.10617/movvol.spmregister.nii'; errfile = './tmp.spmreg.10617/spmregister.10617.err'; fmt = 'nii'; 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 fprintf('fmt %s\n',fmt); which spm_coreg % This is a hack to try to determine which version of spm is being run. If % spm8 is being run with analyze as input, a left-right reveral will occur. % This searches for "spm8" in the spm path, not perfect, but hopefully good % enough. It does not appear that spm offers a "version" command. IsSPM8 = length(findstr(dirname(which('spm_coreg')),'spm8')); if(IsSPM8 & strcmp(fmt,'img')) fprintf('\n\n'); fprintf('ERROR: you appear to be using spm8. If so, re-run this with --nii\n'); fprintf('\n\n'); fp = fopen(errfile,'a'); fprintf(fp,'ERROR: you appear to be using spm8. If so, re-run this with --nii\n'); fclose(fp); return; quit; exit; % These do nothing when run from a csh script end 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 ME fprintf('ERROR: spm_coreg\n'); ME fp = fopen(errfile,'a'); fprintf(fp,'ERROR: spm_coreg (catch)\n'); fprintf(fp,'%s\n',which('spm_coreg')); fprintf(fp,'%s\n',ME.message); fclose(fp); return; quit; end if(isempty(x)) fprintf('ERROR: spm_coreg\n'); if(~monly) fp = fopen(errfile,'a'); fprintf(fp,'ERROR: spm_coreg, x is empty\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'. 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 (R) > Copyright 1984-2012 The MathWorks, Inc. R2012a (7.14.0.739) 64-bit (glnxa64) February 9, 2012 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> >> >> fmt nii >> /autofs/space/lyon_009/pubsw/common/spm/spm8/spm_coreg.m >> >> >> >> >> >> >> >> >> >> Direct calls to spm_defauts are deprecated. Please use spm('Defaults',modality) or spm_get_defaults instead. >> >> INFO: Assuming RAS coordinate system >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> using ./tmp.spmreg.10617/refvol.spmregister.nii as the target image >> using ./tmp.spmreg.10617/movvol.spmregister.nii as the source image >> >> >> >> >> >> >> Error using read_hdr (line 35) Error reading header file "./tmp.spmreg.10617/refvol.spmregister.nii" Error in nifti (line 27) vol = read_hdr(fname); Error in spm_vol_nifti (line 16) N = nifti(fname); Error in spm_vol>subfunc (line 136) V = spm_vol_nifti(p); Error in spm_vol>subfunc1 (line 84) v = subfunc(P(i,:)); Error in spm_vol>subfunc2 (line 70) V = subfunc1(P); Error in spm_vol (line 54) V = subfunc2(P); >> Undefined function or variable 'VG'. >> >> >> Error using read_hdr (line 35) Error reading header file "./tmp.spmreg.10617/movvol.spmregister.nii" Error in nifti (line 27) vol = read_hdr(fname); Error in spm_vol_nifti (line 16) N = nifti(fname); Error in spm_vol>subfunc (line 136) V = spm_vol_nifti(p); Error in spm_vol>subfunc1 (line 84) v = subfunc(P(i,:)); Error in spm_vol>subfunc2 (line 70) V = subfunc1(P); Error in spm_vol (line 54) V = subfunc2(P); >> Undefined function or variable 'VF'. >> >> INFO: ignore warnings about scalefactor >> >> determining coregistration parameters... >> >> >> ERROR: spm_coreg ME = MException Properties: identifier: 'MATLAB:undefinedVarOrFunction' message: 'Undefined variable "VG" or function "VG.fname".' cause: {} stack: [0x1 struct] Error using fclose Invalid file identifier. Use fopen to generate a valid file identifier. >> Undefined function or variable 'x'. >> Finished after 0.188717 sec >> >> Parameters >> Undefined function or variable 'x'. >> >> >> >> >> Undefined function or variable 'x'. >> >> Using spm_get_space Undefined variable "VF" or function "VF.fname". >> >> >> ERROR: matlab exited with errors ERROR: spmregister exited with errors ______________________ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School Psychiatric Neuroimaging Research Program CNY Building 120, suite 100 Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco(a)nmr.mgh.harvard.edu

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Re: [Freesurfer] spmregister error
by Marco Loggia 26 Jul '13

26 Jul '13

Hi again, interestingly, if I run the same command using the full fsvol path I get the 'Disk quota exceeded' message... I wonder if even the message I wrote you about in my previous email has something to do with disk space. I will try free up some room and try spmregister again! Marco bash-4.1$ spmregister --mov "$file".nii --s PBR_"$subj" --reg tmp.dat --fsvol /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz mkdir: cannot create directory `./tmp.spmreg.11238': Disk quota exceeded Log file is ./spmregister.log Fri Jul 26 11:21:20 EDT 2013 tee: ./spmregister.log: Disk quota exceeded --mov rsl_CLBP001_f1_1_3627_5427_nas_suv.nii --s PBR_CLBP001 --reg tmp.dat --fsvol /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz tee: ./spmregister.log: Disk quota exceeded $Id: spmregister,v 1.39.2.1 2012/10/30 20:05:17 greve Exp $ tee: ./spmregister.log: Disk quota exceeded matlab matlab tee: ./spmregister.log: Disk quota exceeded fmt nii tee: ./spmregister.log: Disk quota exceeded UseSPMGetSpace 1 tee: ./spmregister.log: Disk quota exceeded ERROR: /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri//autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz.mgz not found in either COR or MGZ formats > Hello Doug, > > I am encountering the error below when running spmregister. Where do you > think is the issue? Thanks! > > Best, > Marco > > > > bash-4.1$ spmregister --mov "$file".nii --s PBR_"$subj" --reg tmp.dat > --fsvol merged.lrrev > > Log file is ./spmregister.log > Fri Jul 26 10:52:49 EDT 2013 > --mov rsl_CLBP001_f1_1_3627_5427_nas_suv.nii --s PBR_CLBP001 --reg tmp.dat > --fsvol merged.lrrev > $Id: spmregister,v 1.39.2.1 2012/10/30 20:05:17 greve Exp $ > matlab matlab > fmt nii > UseSPMGetSpace 1 > -------------------------------------- > /autofs/cluster/hookerlab/Studies/PBR/Marco/CLBP001/PET/Sum_single_frame/PET_recon_SUV/rsl_files > mri_convert > /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz > ./tmp.spmreg.10617/refvol.spmregister.nii -ic 0 0 0 > mri_convert > /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz > ./tmp.spmreg.10617/refvol.spmregister.nii -ic 0 0 0 > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from > /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz... > TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.0414768, -0.991189, -0.125791) > j_ras = (-0.0799847, 0.128789, -0.988441) > k_ras = (-0.995933, 0.030936, 0.084622) > writing to ./tmp.spmreg.10617/refvol.spmregister.nii... > -------------------------------------- > /autofs/cluster/hookerlab/Studies/PBR/Marco/CLBP001/PET/Sum_single_frame/PET_recon_SUV/rsl_files > mri_convert rsl_CLBP001_f1_1_3627_5427_nas_suv.nii > ./tmp.spmreg.10617/movvol.spmregister.nii -ic 0 0 0 --frame 0 > mri_convert rsl_CLBP001_f1_1_3627_5427_nas_suv.nii > ./tmp.spmreg.10617/movvol.spmregister.nii -ic 0 0 0 --frame 0 > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from rsl_CLBP001_f1_1_3627_5427_nas_suv.nii... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (1, 0, 0) > j_ras = (0, -1, 0) > k_ras = (0, 0, -1) > keeping frame 0 > writing to ./tmp.spmreg.10617/movvol.spmregister.nii... > Matlab file is ./tmp.spmreg.10617/spmregister.10617.m > monly = 0; > targvol = './tmp.spmreg.10617/refvol.spmregister.nii'; > srcvol = './tmp.spmreg.10617/movvol.spmregister.nii'; > errfile = './tmp.spmreg.10617/spmregister.10617.err'; > fmt = 'nii'; > > 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 > > fprintf('fmt %s\n',fmt); > which spm_coreg > > % This is a hack to try to determine which version of spm is being run. If > % spm8 is being run with analyze as input, a left-right reveral will > occur. > % This searches for "spm8" in the spm path, not perfect, but hopefully > good > % enough. It does not appear that spm offers a "version" command. > IsSPM8 = length(findstr(dirname(which('spm_coreg')),'spm8')); > if(IsSPM8 & strcmp(fmt,'img')) > fprintf('\n\n'); > fprintf('ERROR: you appear to be using spm8. If so, re-run this with > --nii\n'); > fprintf('\n\n'); > fp = fopen(errfile,'a'); > fprintf(fp,'ERROR: you appear to be using spm8. If so, re-run this with > --nii\n'); > fclose(fp); > return; quit; exit; % These do nothing when run from a csh script > end > > 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 ME > fprintf('ERROR: spm_coreg\n'); > ME > fp = fopen(errfile,'a'); > fprintf(fp,'ERROR: spm_coreg (catch)\n'); > fprintf(fp,'%s\n',which('spm_coreg')); > fprintf(fp,'%s\n',ME.message); > fclose(fp); > return; quit; > end > if(isempty(x)) > fprintf('ERROR: spm_coreg\n'); > if(~monly) > fp = fopen(errfile,'a'); > fprintf(fp,'ERROR: spm_coreg, x is empty\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'. 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 (R) > > Copyright 1984-2012 The MathWorks, Inc. > R2012a (7.14.0.739) 64-bit (glnxa64) > February 9, 2012 > > > To get started, type one of these: helpwin, helpdesk, or demo. > For product information, visit www.mathworks.com. > >>> >> >> >> >> >> >> >> >> fmt nii >>> /autofs/space/lyon_009/pubsw/common/spm/spm8/spm_coreg.m >>> >> >> >> >> >> >> >> >> >> Direct calls to spm_defauts are deprecated. > Please use spm('Defaults',modality) or spm_get_defaults instead. >>> >> INFO: Assuming RAS coordinate system >>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> using > ./tmp.spmreg.10617/refvol.spmregister.nii > as the target > image >>> using ./tmp.spmreg.10617/movvol.spmregister.nii as the source image >>> >> >> >> >> >> >> Error using read_hdr (line 35) > Error reading header file "./tmp.spmreg.10617/refvol.spmregister.nii" > > Error in nifti (line 27) > vol = read_hdr(fname); > > Error in spm_vol_nifti (line 16) > N = nifti(fname); > > Error in spm_vol>subfunc (line 136) > V = spm_vol_nifti(p); > > Error in spm_vol>subfunc1 (line 84) > v = subfunc(P(i,:)); > > Error in spm_vol>subfunc2 (line 70) > V = subfunc1(P); > > Error in spm_vol (line 54) > V = subfunc2(P); > >>> Undefined function or variable 'VG'. > >>> >> >> Error using read_hdr (line 35) > Error reading header file "./tmp.spmreg.10617/movvol.spmregister.nii" > > Error in nifti (line 27) > vol = read_hdr(fname); > > Error in spm_vol_nifti (line 16) > N = nifti(fname); > > Error in spm_vol>subfunc (line 136) > V = spm_vol_nifti(p); > > Error in spm_vol>subfunc1 (line 84) > v = subfunc(P(i,:)); > > Error in spm_vol>subfunc2 (line 70) > V = subfunc1(P); > > Error in spm_vol (line 54) > V = subfunc2(P); > >>> Undefined function or variable 'VF'. > >>> >> > > INFO: ignore warnings about scalefactor > >>> >> determining coregistration parameters... >>> >> >> ERROR: spm_coreg > > ME = > > MException > > Properties: > identifier: 'MATLAB:undefinedVarOrFunction' > message: 'Undefined variable "VG" or function "VG.fname".' > cause: {} > stack: [0x1 struct] > > > Error using fclose > Invalid file identifier. Use fopen to generate a valid file identifier. > >>> Undefined function or variable 'x'. > >>> Finished after 0.188717 sec >>> >> Parameters >> Undefined function or variable 'x'. > >>> >>> >> >> >> Undefined function or variable 'x'. > >>> >> Using spm_get_space > Undefined variable "VF" or function "VF.fname". > >>> >> >> ERROR: matlab exited with errors > ERROR: spmregister exited with errors > > > ______________________ > > Marco L. Loggia, PhD > Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital > Harvard Medical School > > Psychiatric Neuroimaging Research Program > CNY Building 120, suite 100 > Charlestown, Massachusetts 02129 > Phone: (617) 643-7267 > Fax: (617) 643-7340 > marco(a)nmr.mgh.harvard.edu > ______________________ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School Psychiatric Neuroimaging Research Program CNY Building 120, suite 100 Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco(a)nmr.mgh.harvard.edu

2 1

correspondance between broadmann areas and freesurfer labels
by LAOUCHEDI MAKHLOUF 26 Jul '13

26 Jul '13

Hi i used freesurfer labels in a study and i want to identify the broadmann areas corresponding to some labels, is there any correspondence between the two ? Thanks

4 10

Re: [Freesurfer] bug reporting
by Douglas Greve 25 Jul '13

25 Jul '13

Do you have permissions to the file? If so, rerun recon-all with -debug as the first option, then send the terminal output to the list. doug ps. Please send emails to the list and not to us individually. thanks! On 7/25/13 2:31 PM, Kyllo, Hannah M wrote: > yes > > - Hannah Kyllo > ------------------------------------------------------------------------ > *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu > [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas Greve > [greve(a)nmr.mgh.harvard.edu] > *Sent:* Thursday, July 25, 2013 11:46 AM > *To:* freesurfer(a)nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] bug reporting > > > Does subj001.nii.gz exist in the folder you ran recon-all from? > > > On 7/25/13 12:21 PM, Kyllo, Hannah M wrote: >> Hello, >> >> I've received the following error using Ubuntu 13.04: >> >> "WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! >> >> ERROR: cannot find subj001.nii.gz >> Linux neuron 3.2.0-49-generic #75-Ubuntu SMP Tue Jun 18 17:39:32 UTC >> 2013 x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s exited with ERRORS at Thu Jul 25 11:15:50 CDT 2013" >> >> thanks in advance for your input, >> >> - Hannah Kyllo >> >> The information in this e-mail may be privileged and confidential, >> intended only for the use of the addressee(s) above. Any unauthorized >> use or disclosure of this information is prohibited. If you have >> received this e-mail by mistake, please delete it and immediately >> contact the sender. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

1 0

MRI_Convert error
by Pom Sailasuta 25 Jul '13

25 Jul '13

Hello, I am resending this post since there is no reply for 2 days, I really appreciate your help. thanks so much. I have several errors using mri_convert to convert 3T Philips T1-wt, DTI and fMRI images. The last one on T1-wt images tells me to send email to freesurfer, so here is the error messages: [pom@PomLinux /home/pom]% !mri mri_convert -it dicom -i IM_0001 -ot mgz -o 001.mgz mri_convert -it dicom -i IM_0001 -ot mgz -o 001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from IM_0001... Starting DICOMRead2() dcmfile = /home/pom/Software/freesurfer/ subjects/S009002A/mri/orig/orig2/IM_0001 dcmdir = /home/pom/Software/freesurfer/subjects/S009002A/mri/orig/orig2 WARNING: tag image orientation not found Ref Series No = 2 ERROR: bits = 8 not supported. Send email to freesurfer(a)nmr.mgh.harvard.edu for DTI images, here is the errors: MRIalloc(0, 0, 1855): bad parm [pom@PomLinux /home/pom]% mri_convert -it dicom -i IM_0001 -ot mgz -o 001.mgz mri_convert -it dicom -i IM_0001 -ot mgz -o 001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from IM_0001... Starting DICOMRead2() dcmfile = /home/pom/Software/freesurfer/subjects/S009002A/mri/orig/IM_0001 dcmdir = /home/pom/Software/freesurfer/subjects/S009002A/mri/orig Ref Series No = 501 Found 1874 files, checking for dicoms WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag SeriesNumber not found WARNING: tag image orientation not found Found 1855 dicom files in series. WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag SeriesNumber not found WARNING: tag image orientation not found First Sorting Computing Slice Direction Vs: -117.09 -112.869 17.456 Vs: -0.715854 -0.690047 0.106721 Second Sorting Counting frames nframes = 1 nslices = 1855 ndcmfiles = 1855 MRIalloc(0, 0, 1855): bad parm ERROR: mri alloc failed I would greatly appreciate any help. -- Pom

2 2

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Freesurfer