Re: [Freesurfer] spmregister error
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
Re: [Freesurfer] spmregister error
That probably just means that you have run out of space in the directory
you are running it from. Run
quota -v
to see
doug
On 7/26/13 11:27 AM, Marco Loggia wrote:
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
Re: [Freesurfer] spmregister error
what version of spm are you using? Look in your ~/matlab/startup.m file
to see. If you are using version 5 or less, then add --img
doug
On 7/26/13 11:19 AM, Marco Loggia wrote:
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 =
Re: [Freesurfer] spmregister error
Make sure that there is an orig.mgz in $SUBJECTS_DIR/MGXX_SurferOutput/mri Also, make sure to send the full terminal output doug On 03/28/2013 02:13 PM, Borzello, Mia wrote: Hi Freesurfers, I'm in the middle of coregistering a CT and MRI, and after running spmregister --s MGXX_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig I get the error that orig.mgz is not found in COR or MGZ formats, but I have an orig.mgz file in my folder. Any help on this would be awesome! Thanks, Mia ___ 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 gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] spmregister error
package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg Two suggestions: 1. Can you temporarily change the spm path to spm5 to see if that fixes the problem? 2. Can you send me your command line, directory you ran it from, SUBJECTS_DIR, and terminal output? doug Chindhuri Selvadurai wrote: The path to spm2 was not originally in my startup.m file, but even when I added it, it didn't work. I am using 7.8, but I tried to change my cshrc file back to 7.1 however, once I ran the script, it was actually running 7.4 Thank you, Chindhuri Chindhuri, Is the path to spm2 added in your startup.m file and are you using matlab 7.1 (required by spm2)? doug Chindhuri Selvadurai wrote: Hello, I am getting the same error that was discussed in the attached thread, however, the addition of the path line did not work for me. I am also not sure if we should be using spm5 since all in the past we have been using spm2. It presents this error when running under my name, but not for other users. Any help would be appreciated! Thanks, Chindhuri Re: [Freesurfer] spmregister error Douglas N Greve Fri, 30 Jul 2010 09:58:18 -0700 Yes, that should work. doug Adam Nitenson wrote: Hi Sandra, I just had this same problem about a week ago. The solution which worked for me was adding the following line of text into the startup.m file in your matlab folder: path(path,'/usr/pubsw/common/spm/spm5'); I'm not sure it matter exactly where you put it. I put mine in the last row in the FreeSurfer FAST section, under the line beginning with clear. Hope that helps! -Adam Hello, When running spmregister-sess (standard environment was sourced) I encountered this error: ERROR: matlab exited with errors ERROR: cannot find spm_coreg.m. Make sure that the SPM package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg ERROR: spmregister failed __ Our information: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.7.1.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: purkinje SUBJECTS_DIR: /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons PWD: /cluster/ablood/1/DMRF_ASL ssh purkinje setenv SUBJECTS_DIR /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons cd /cluster/ablood/1/DMRF_ASL __ We appreciate any help you can give us!! Thanks, Sandra Mood and Motor Control Laboratory Athinoula Martinos Center for Biomedical Imaging Massachusetts General Hospital 120 6th St. Charlestown, MA 02129 Tel: 617-643-6245 Fax: 617-726-1351 Email: swoodm...@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 gr...@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 gr...@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 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.
Re: [Freesurfer] spmregister error
/tmp.bbregister.26962/spmregister/movvol.spmregister.img as the source image ??? Undefined function or method 'spm_vol' for input arguments of type 'char'. ??? Undefined function or variable 'VG'. ??? Undefined function or method 'spm_vol' for input arguments of type 'char'. ??? Undefined function or variable 'VF'. INFO: ignore warnings about scalefactor determining coregistration parameters... ERROR: spm_coreg ??? Undefined function or variable 'x'. Finished after 0.008886 sec Parameters ??? Undefined function or variable 'x'. ??? Undefined function or variable 'x'. Using spm_get_space ??? Undefined variable VF or class VF.fname. ERROR: matlab exited with errors ERROR: cannot find spm_coreg.m. Make sure that the SPM package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg Two suggestions: 1. Can you temporarily change the spm path to spm5 to see if that fixes the problem? 2. Can you send me your command line, directory you ran it from, SUBJECTS_DIR, and terminal output? doug Chindhuri Selvadurai wrote: The path to spm2 was not originally in my startup.m file, but even when I added it, it didn't work. I am using 7.8, but I tried to change my cshrc file back to 7.1 however, once I ran the script, it was actually running 7.4 Thank you, Chindhuri Chindhuri, Is the path to spm2 added in your startup.m file and are you using matlab 7.1 (required by spm2)? doug Chindhuri Selvadurai wrote: Hello, I am getting the same error that was discussed in the attached thread, however, the addition of the path line did not work for me. I am also not sure if we should be using spm5 since all in the past we have been using spm2. It presents this error when running under my name, but not for other users. Any help would be appreciated! Thanks, Chindhuri Re: [Freesurfer] spmregister error Douglas N Greve Fri, 30 Jul 2010 09:58:18 -0700 Yes, that should work. doug Adam Nitenson wrote: Hi Sandra, I just had this same problem about a week ago. The solution which worked for me was adding the following line of text into the startup.m file in your matlab folder: path(path,'/usr/pubsw/common/spm/spm5'); I'm not sure it matter exactly where you put it. I put mine in the last row in the FreeSurfer FAST section, under the line beginning with clear. Hope that helps! -Adam Hello, When running spmregister-sess (standard environment was sourced) I encountered this error: ERROR: matlab exited with errors ERROR: cannot find spm_coreg.m. Make sure that the SPM package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg ERROR: spmregister failed __ Our information: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.7.1.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: purkinje SUBJECTS_DIR: /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons PWD: /cluster/ablood/1/DMRF_ASL ssh purkinje setenv SUBJECTS_DIR /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons cd /cluster/ablood/1/DMRF_ASL __ We appreciate any help you can give us!! Thanks, Sandra Mood and Motor Control Laboratory Athinoula Martinos Center for Biomedical Imaging Massachusetts General Hospital 120 6th St. Charlestown, MA 02129 Tel: 617-643-6245 Fax: 617-726-1351 Email: swoodm...@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 gr...@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
Re: [Freesurfer] spmregister error
Two suggestions: 1. Can you temporarily change the spm path to spm5 to see if that fixes the problem? 2. Can you send me your command line, directory you ran it from, SUBJECTS_DIR, and terminal output? doug Chindhuri Selvadurai wrote: The path to spm2 was not originally in my startup.m file, but even when I added it, it didn't work. I am using 7.8, but I tried to change my cshrc file back to 7.1 however, once I ran the script, it was actually running 7.4 Thank you, Chindhuri Chindhuri, Is the path to spm2 added in your startup.m file and are you using matlab 7.1 (required by spm2)? doug Chindhuri Selvadurai wrote: Hello, I am getting the same error that was discussed in the attached thread, however, the addition of the path line did not work for me. I am also not sure if we should be using spm5 since all in the past we have been using spm2. It presents this error when running under my name, but not for other users. Any help would be appreciated! Thanks, Chindhuri Re: [Freesurfer] spmregister error Douglas N Greve Fri, 30 Jul 2010 09:58:18 -0700 Yes, that should work. doug Adam Nitenson wrote: Hi Sandra, I just had this same problem about a week ago. The solution which worked for me was adding the following line of text into the startup.m file in your matlab folder: path(path,'/usr/pubsw/common/spm/spm5'); I'm not sure it matter exactly where you put it. I put mine in the last row in the FreeSurfer FAST section, under the line beginning with clear. Hope that helps! -Adam Hello, When running spmregister-sess (standard environment was sourced) I encountered this error: ERROR: matlab exited with errors ERROR: cannot find spm_coreg.m. Make sure that the SPM package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg ERROR: spmregister failed __ Our information: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.7.1.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: purkinje SUBJECTS_DIR: /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons PWD: /cluster/ablood/1/DMRF_ASL ssh purkinje setenv SUBJECTS_DIR /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons cd /cluster/ablood/1/DMRF_ASL __ We appreciate any help you can give us!! Thanks, Sandra Mood and Motor Control Laboratory Athinoula Martinos Center for Biomedical Imaging Massachusetts General Hospital 120 6th St. Charlestown, MA 02129 Tel: 617-643-6245 Fax: 617-726-1351 Email: swoodm...@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 gr...@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 gr...@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 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] spmregister error
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 gr...@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 ___ Freesurfer mailing list Freesurfer@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. * [Freesurfer] spmregister error swoodman o Re: [Freesurfer] spmregister error Adam Nitenson + Re: [Freesurfer] spmregister error Douglas N Greve # Re: [Freesurfer] spmregister error swoodman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] spmregister error
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 gr...@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 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] spmregister error
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 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.
Re: [Freesurfer] spmregister error
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 gr...@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 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] spmregister error
That seems to now work with those changes. Thanks so much to Adam and Doug! Sandra 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 gr...@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 ___ Freesurfer mailing list Freesurfer@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.
