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:
- Can you temporarily change the spm path to spm5 to see if that fixes
the problem?
- 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...@partners.org _______________________________________________ Freesurfer mailing list Freesurfer@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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@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
Did you happen to notice this error printed by matlab?
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'.
Try removing this line in your startup.m and re-running.
doug
Chindhuri Selvadurai wrote:
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, 2007To 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:
- Can you temporarily change the spm path to spm5 to see if that fixes
the problem?
- 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...@partners.org > _______________________________________________ > Freesurfer mailing list > Freesurfer@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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@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
Hi all,
I am encountering a similar error with spmregister, although it is a bit different. When my startup.m is configured to add the SPM2 paths, spmregister works without issue. However, when my startup.m uses either the SPM5 or 8 paths, it fails with the following error:
Welcome to MATLAB
>> >> >> >> >> >> /usr/pubsw/common/spm/spm8/spm_coreg.m >> >> INFO: Assuming RAS coordinate system >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> using
./tmp.bbregister.6451/spmregister/refvol.spmregister.img as the target image
using ./tmp.bbregister.6451/spmregister/movvol.spmregister.img as
the source image
>> >> >> >> ??? Undefined function or method 'spm_vol_ana' for
input arguments of type 'char'.
Error in ==> spm_vol>subfunc at 94 if isempty(n), V = spm_vol_ana(p);
Error in ==> spm_vol>subfunc1 at 63 v = subfunc(P(i,:));
Error in ==> spm_vol>subfunc2 at 52 V = subfunc1(P);
Error in ==> spm_vol at 38 V = subfunc2(P);
??? Undefined function or variable 'VG'.
??? Undefined function or method 'spm_vol_ana' for input
arguments of type 'char'.
Error in ==> spm_vol>subfunc at 94 if isempty(n), V = spm_vol_ana(p);
Error in ==> spm_vol>subfunc1 at 63 v = subfunc(P(i,:));
Error in ==> spm_vol>subfunc2 at 52 V = subfunc1(P);
Error in ==> spm_vol at 38 V = subfunc2(P);
??? Undefined function or variable 'VF'.
INFO: ignore warnings about scalefactor
determining coregistration parameters...
ERROR: spm_coreg
??? Undefined function or variable 'x'.
Finished after 0.029568 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: spm_coreg /usr/pubsw/common/spm/spm8/spm_coreg.m
We analyze using SPM8, so I'd prefer not to have to switch my startup.m to the SPM2 paths every time I want to register a subject.
Thanks for your help!
Andy
Chindhuri Selvadurai wrote:
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, 2007To 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:
- Can you temporarily change the spm path to spm5 to see if that fixes
the problem?
- 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...@partners.org > _______________________________________________ > Freesurfer mailing list > Freesurfer@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Chindhuri Selvadurai -
Douglas N Greve