Hello,
Changing the spm path to spm5 did not fix the problem.
Command line: bbregister --s RMCON051 --mov ../bold/009/f.nii --reg
../bold/register.dat
--init-spm --bold
Scripts directory: /space/ventzl/36/users/RespMon12C/scripts
SUBJECTS_DIR: /space/ventzl/36/users/RespMon12C/subjects
terminal output:
vantz:chinsel[102] nmrenv
-------- freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer/stable4
FSFAST_HOME /usr/local/freesurfer/stable4/fsfast
FSF_OUTPUT_FORMAT nii
SUBJECTS_DIR /space/ventzl/36/users/RespMon12C/subjects
MNI_DIR /usr/local/freesurfer/stable4/mni
FSL_DIR /usr/pubsw/packages/fsl/current
[vantz:scripts] (nmr-std-env) pwd
/autofs/space/ventzl_036/users/RespMon12C/scripts
[vantz:scripts] (nmr-std-env) ./ bbregister.bash
./: Permission denied.
[vantz:scripts] (nmr-std-env) ./bbregister.bash
Log file is ../bold/register.dat.log
Thu Oct 7 10:07:04 EDT 2010
setenv SUBJECTS_DIR /space/ventzl/36/users/RespMon12C/subjects
cd /autofs/space/ventzl_036/users/RespMon12C/subjects/RMCON051/mystudy
/usr/local/freesurfer/stable4/bin/bbregister --s RMCON051 --mov
../bold/009/f.nii --reg ../bold/register.dat --init-spm --bold
$Id: bbregister,v 1.14.2.13 2009/12/16 20:20:09 greve Exp $
Linux vantz 2.6.18-194.8.1.el5 #1 SMP Thu Jul 1 19:04:48 EDT 2010 x86_64
x86_64 x86_64 GNU/Linux
FREESURFER_HOME /usr/local/freesurfer/stable4
mri_convert ../bold/009/f.nii ../bold/tmp.bbregister.26962/template.nii
mri_convert ../bold/009/f.nii ../bold/tmp.bbregister.26962/template.nii
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from ../bold/009/f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.997195, -0.0748521, -0.000274916)
j_ras = (0.0748328, -0.997009, 0.0193167)
k_ras = (-0.00171999, 0.0192419, 0.999813)
writing to ../bold/tmp.bbregister.26962/template.nii...
spmregister --s RMCON051 --mov ../bold/tmp.bbregister.26962/template.nii
--reg ../bold/tmp.bbregister.26962/reg.init.dat --tmp
../bold/tmp.bbregister.26962/spmregister
Log file is ../bold/tmp.bbregister.26962/spmregister.log
Thu Oct 7 10:07:14 EDT 2010
--s RMCON051 --mov ../bold/tmp.bbregister.26962/template.nii --reg
../bold/tmp.bbregister.26962/reg.init.dat --tmp
../bold/tmp.bbregister.26962/spmregister
$Id: spmregister,v 1.21.2.5 2009/04/15 18:10:23 greve Exp $
matlab matlab
fmt img
UseSPMGetSpace 1
--------------------------------------
/autofs/space/ventzl_036/users/RespMon12C/subjects/RMCON051/mystudy
mri_convert
/space/ventzl/36/users/RespMon12C/subjects/RMCON051/mri/brainmask.mgz
../bold/tmp.bbregister.26962/spmregister/refvol.spmregister.img -ic 0 0 0
mri_convert
/space/ventzl/36/users/RespMon12C/subjects/RMCON051/mri/brainmask.mgz
../bold/tmp.bbregister.26962/spmregister/refvol.spmregister.img -ic 0 0 0
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from
/space/ventzl/36/users/RespMon12C/subjects/RMCON051/mri/brainmask.mgz...
TR=2530.00, TE=1.64, TI=1200.00, flip angle=7.00
i_ras = (-1, -1.49012e-08, -2.12167e-08)
j_ras = (-9.8953e-08, -7.69251e-09, -1)
k_ras = (3.72529e-08, 1, 4.14548e-09)
writing to
../bold/tmp.bbregister.26962/spmregister/refvol.spmregister.img... Analyze
Output Matrix
-1.000 -0.000 0.000 129.000;
-0.000 -0.000 1.000 -129.000;
-0.000 -1.000 0.000 129.000;
0.000 0.000 0.000 1.000;
--------------------
INFO: set hdr.hist.orient to -1
--------------------------------------
/autofs/space/ventzl_036/users/RespMon12C/subjects/RMCON051/mystudy
mri_convert ../bold/tmp.bbregister.26962/template.nii
../bold/tmp.bbregister.26962/spmregister/movvol.spmregister.img -ic 0 0 0
--frame 0
mri_convert ../bold/tmp.bbregister.26962/template.nii
../bold/tmp.bbregister.26962/spmregister/movvol.spmregister.img -ic 0 0 0
--frame 0
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from ../bold/tmp.bbregister.26962/template.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.997195, -0.0748521, -0.000274916)
j_ras = (0.0748328, -0.997009, 0.0193167)
k_ras = (-0.00171999, 0.0192419, 0.999813)
keeping frame 0
writing to
../bold/tmp.bbregister.26962/spmregister/movvol.spmregister.img... Analyze
Output Matrix
-3.116 0.234 -0.006 95.227;
-0.234 -3.116 0.071 109.325;
-0.001 0.060 3.699 -64.852;
0.000 0.000 0.000 1.000;
--------------------
INFO: set hdr.hist.orient to -1
Matlab file is
../bold/tmp.bbregister.26962/spmregister/spmregister.27005.m
monly = 0;
targvol =
'../bold/tmp.bbregister.26962/spmregister/refvol.spmregister.img'; srcvol =
'../bold/tmp.bbregister.26962/spmregister/movvol.spmregister.img'; errfile =
'../bold/tmp.bbregister.26962/spmregister/spmregister.27005.err';
if(exist('spm_coreg') ~= 2)
fprintf('ERROR: cannot find spm_coreg.m. Make sure that the SPM\n');
fprintf(' package is in your matlab path (check ~/matlab/startup)\n');
fp = fopen(errfile,'w');
fprintf(fp,'ERROR: cannot find spm_coreg.m. Make sure that the SPM\n');
fprintf(fp,' package is in your matlab path (check
~/matlab/startup)\n');
fclose(fp);
return; quit;
end
which spm_coreg
global defaults
spm_defaults % load spm2's default fields
fprintf('INFO: Assuming RAS coordinate system\n');
defaults.analyze.flip = 0;
%===========================================================================
% coregistration defaults
%===========================================================================
defaults.coreg.estimate.cost_fun = 'nmi';
defaults.coreg.estimate.sep = [4 2];
defaults.coreg.estimate.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01
0.01 0.01 0.001 0.001 0.001];
defaults.coreg.estimate.fwhm = [7 7];
defaults.coreg.estimate.params = [0 0 0 0 0 0];
defaults.coreg.estimate.graphics = 0; % dont crate ps file
%===========================================================================
% coregister files
%===========================================================================
disp(sprintf('using %s as the target image',targvol));
disp(sprintf('using %s as the source image',srcvol));
[pth1,nam1,ext1] = fileparts(deblank(targvol));
[pth2,nam2,ext2] = fileparts(deblank(srcvol));
%tmp = spm_get('Files',pth1,[nam1 ext1]);
tmp = sprintf('%s/%s%s',pth1,nam1,ext1);
VG = spm_vol(tmp); % target image
if(isempty(VG))
fprintf('ERROR: loading target %s\n',targvol);
fp = fopen(errfile,'a');
fprintf(fp,'ERROR: loading target %s\n',targvol);
fclose(fp);
return; quit;
end
% tmp = spm_get('Files',pth2,[nam2 ext2])
tmp = sprintf('%s/%s%s',pth2,nam2,ext2);
VF = spm_vol(tmp); % source image
if(isempty(VF))
fprintf('ERROR: loading source %s\n',srcvol);
fp = fopen(errfile,'a');
fprintf(fp,'ERROR: loading source %s\n',srcvol);
fclose(fp);
return; quit;
end
fprintf('\n\nINFO: ignore warnings about scalefactor\n\n');
disp('determining coregistration parameters...')
tic;
try
x = spm_coreg(VG.fname,VF.fname,defaults.coreg.estimate);
catch
fprintf('ERROR: spm_coreg\n');
fp = fopen(errfile,'a');
fprintf(fp,'ERROR: spm_coreg\n');
fprintf(fp,'%s\n',which('spm_coreg'));
fclose(fp);
return; quit;
end
if(isempty(x))
fprintf('ERROR: spm_coreg\n');
if(~monly)
fp = fopen(errfile,'a');
fprintf(fp,'ERROR: spm_coreg\n');
fclose(fp);
return; quit;
end
end
fprintf('Finished after %g sec\n',toc);
fprintf('Parameters ');
fprintf('%g ',x);
fprintf('\n');
%---------write out the .mat file---see spm_coreg_ui.m line 283
M = inv(spm_matrix(x));
if(1)
fprintf('Using spm_get_space\n');
MM = zeros(4,4,1);
MM = spm_get_space(deblank(VF.fname));
spm_get_space(deblank(VF.fname), M*MM);
fprintf('\n\nINFO: ignore warnings about scalefactor\n\n');
else
fprintf('Using MRIread/write instead of spm_get_space\n');
ff = MRIread(deblank(VF.fname));
ff.vox2ras1 = M*ff.vox2ras1;
ff.vox2ras0 = vox2ras_1to0(ff.vox2ras1);
ff.vox2ras = ff.vox2ras0;
MRIwrite(ff,deblank(VF.fname));
end
return;
if(~monly) quit; end
Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.
Warning: No window system found. Java option 'MWT' ignored
< M A T L A B >
Copyright 1984-2007 The MathWorks, Inc.
Version 7.4.0.287 (R2007a)
January 29, 2007
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Warning: Executing startup failed in matlabrc.
This indicates a potentially serious problem in your MATLAB setup, which
should be resolved as soon as possible. Error detected was:
MATLAB:UndefinedFunction
Undefined function or variable 'mne_setup_toolbox'.
> In matlabrc at 259
>> >> >> >> >> >> >> ERROR: cannot find spm_coreg.m. Make sure that the
SPM
package is in your matlab path (check ~/matlab/startup)
>> >> 'spm_coreg' not found.
>> >> >> ??? Undefined function or variable 'spm_defaults'.
>> >> INFO: Assuming RAS coordinate system
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> using
../bold/tmp.bbregister.26962/spmregister/refvol.spmregister.img
as the target
image
>> using ../bold/tmp.bbregister.26962/spmregister/movvol.spmregister.img
as the source image
>> >> >> >> >> >> >> ??? Undefined function or method 'spm_vol' for input
arguments of type 'char'.
>> ??? Undefined function or variable 'VG'.
>> >> >> ??? Undefined function or method 'spm_vol' for input arguments of
type 'char'.
>> ??? Undefined function or variable 'VF'.
>> >>
INFO: ignore warnings about scalefactor
>> >> determining coregistration parameters...
>> >> >> ERROR: spm_coreg
>> ??? Undefined function or variable 'x'.
>> Finished after 0.008886 sec
>> >> Parameters >> ??? Undefined function or variable 'x'.
>>
>> >> >> >> ??? Undefined function or variable 'x'.
>> >> Using spm_get_space
??? Undefined variable "VF" or class "VF.fname".
>> >> >> ERROR: matlab exited with errors
ERROR: cannot find spm_coreg.m. Make sure that the SPM
package is in your matlab path (check ~/matlab/startup)
ERROR: spm_coreg
> Two suggestions:
> 1. Can you temporarily change the spm path to spm5 to see if that fixes
the problem?
> 2. Can you send me your command line, directory you ran it from,
SUBJECTS_DIR, and terminal output?
> doug
> Chindhuri Selvadurai wrote:
>> The path to spm2 was not originally in my startup.m file, but even when
I added it, it didn't work.
>> I am using 7.8, but I tried to change my cshrc file back to 7.1
however,
>> once I ran the script, it was actually running 7.4
>> Thank you,
>> Chindhuri
>>> Chindhuri,
>>> Is the path to spm2 added in your startup.m file and are you using
>> matlab 7.1 (required by spm2)?
>>> doug
>>> Chindhuri Selvadurai wrote:
>>>> Hello,
>>>> I am getting the same error that was discussed in the attached
thread,
>> however, the addition of the path line did not work for me.
>>>> I am also not sure if we should be using spm5 since all in the past
we
>> have been using spm2. It presents this error when running under my
name,
>>>> but not for other users.
>>>> Any help would be appreciated!
>>>> Thanks,
>>>> Chindhuri
>>>> ________________________________________________
>>>> Re: [Freesurfer] spmregister error
>>>> Douglas N Greve
>>>> Fri, 30 Jul 2010 09:58:18 -0700
>>>> Yes, that should work.
>>>> doug
>>>> Adam Nitenson wrote:
>>>>> Hi Sandra,
>>>>> I just had this same problem about a week ago. The solution
which
>>>>> worked for me was adding the following line of text into the
startup.m
>> file in your matlab folder:
>>>>> path(path,'/usr/pubsw/common/spm/spm5');
>>>>> I'm not sure it matter exactly where you put it. I put mine in the
>> last
>>>>> row in the FreeSurfer FAST section, under the line beginning with
>> "clear".
>>>>> Hope that helps!
>>>>> -Adam
>>>>>> Hello,
>>>>>> When running spmregister-sess (standard environment was sourced) I
>> encountered this error:
>>>>>> ERROR: matlab exited with errors
>>>>>> ERROR: cannot find spm_coreg.m. Make sure that the SPM
>>>>>> package is in your matlab path (check ~/matlab/startup)
>>>>>> ERROR: spm_coreg
>>>>>> ERROR: spmregister failed
>>>>>> __________________________________________________________
>>>>>> Our information:
>>>>>> FREESURFER_HOME: /usr/local/freesurfer/stable4
>>>>>> Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311
>> RedHat release: CentOS release 5.3 (Final)
>>>>>> Kernel info: Linux 2.6.18-128.7.1.el5 x86_64
>>>>>> NMR Center info (/space/freesurfer exists):
>>>>>> machine: purkinje
>>>>>> SUBJECTS_DIR: /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons
>>>>>> PWD: /cluster/ablood/1/DMRF_ASL
>>>>>> ssh purkinje
>>>>>> setenv SUBJECTS_DIR /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons cd
>> /cluster/ablood/1/DMRF_ASL
>>>>>> __________________________________________________________________
We
>> appreciate any help you can give us!!
>>>>>> Thanks,
>>>>>> Sandra
>>>>>> Mood and Motor Control Laboratory
>>>>>> Athinoula Martinos Center for Biomedical Imaging
>>>>>> Massachusetts General Hospital
>>>>>> 120 6th St.
>>>>>> Charlestown, MA 02129
>>>>>> Tel: 617-643-6245
>>>>>> Fax: 617-726-1351
>>>>>> Email: swoodm...@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
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