Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

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

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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 >

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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

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need help
by Haielom Embaie 25 Jul '13

25 Jul '13

Hi there, I was trying to learn the freesurfer, I have hard time to download at the beginning, later after that, I also have no knowledge of how to import images and analyse them. I really need your help tremendously. Thanks, Haielom

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bug reporting
by Kyllo, Hannah M 25 Jul '13

25 Jul '13

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.

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FreeSurfer Version
by Rodrigo Perea 25 Jul '13

25 Jul '13

Is there any other way I can find the FreeSurfer version I am using? According to https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.HowdoIkno… I have to run: recon-all -version, but I get the output below. Now the stable FreeSurfer Version is 5.3.0 so its not even close to the output. Any help? Rodrigo OUTPUT: recon-all -version $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $

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different results between 5.1.0 and 5.2.0
by clarissa yasuda 25 Jul '13

25 Jul '13

Dear FreeSurfer Experts As in some other posts, I have also observed some differences between the two releases. The values from cuneus (thickness) are similar to the post from Ritobrato Datta, Ph.D. on 18 march. But I also observed some differences in volume of right / left thalami. Did anybody observe such asymmetry?? I am now running analysis with patients and controls on data from 5.2.0 and got surprised with this asymmetry. Here I am showing the average I obtained: R PALLIDUM L PALLIDUM R THAL L THAL RH_CUNEUS LH_CUNEUS 5.1 (350 SUBJECTS) 1580 1688 6701 6970.31 1.845 1.857 5.2 (115 SUBJECTS, subgroup of 350) 1519 1367 6520 7401 2.42 2.40 Is there any approach to correct it on 5.2 ?? Thanks in advance clarissa

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R: Re: R: Re: problem with nu_correct
by Andrea Tateo 25 Jul '13

25 Jul '13

Normal 0 14 false false false IT X-NONE X-NONE MicrosoftInternetExplorer4 Hello Zeke, I must make a clarification: I use freesurfer on a PC cluster. I have submitted the same image several times and on different machines. Sometimes it was killed sometimes not. If I submit a second time the failed job it may happen that it is terminated with success. thank you very much /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabella normale"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0cm; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin;} ----Messaggio originale---- Da: zkaufman(a)nmr.mgh.harvard.edu Data: 24-lug-2013 21.53 A: "Andrea Tateo"<andrea.tateo(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: R: Re: [Freesurfer] problem with nu_correct Andrea, Hmmm. I am not able to duplicate this error on my end using local data. A few things: 1) What happens when you type "nu_evaluate -help"? Do you get help output or does it crash? 2) Does this error occur for all subjects or just this one used for this particular recon? 3) Does the brain image look "normal", meaning is there anything obviously wrong with the input data, which you can see by opening it with Freeview? -Zeke On 07/24/2013 11:22 AM, Andrea Tateo wrote: > Hello zkaufman, > > thanks for your involvement > > Andrea > > > > ----Messaggio originale---- > Da: zkaufman(a)nmr.mgh.harvard.edu > Data: 24-lug-2013 16.52 > A: "Andrea Tateo"<andrea.tateo(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] problem with nu_correct > > Hello Andrea, > > Can you please attach the entire recon-all.log file? It will be located > in $SUBJECT_DIR/subject_name/scripts/recon-all.log > > -Zeke > > On 07/24/2013 09:35 AM, Andrea Tateo wrote: > > Hi FreeSurfer expert, > > > > I have a problem with command "recon-all". > > > > In recon-all.log I can to read > > > > nu_correct: crashed while running nu_evaluate (termination status=9) > > > > Thank for your help > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > >

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