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, 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
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
--
Andrew Ward
Brigham and Women's Hospital (BBNG)
Massachusetts General Hospital (GRU)
Athinoula A. Martinos Center for Biomedical Imaging
149 13th St., Room 2689C
Charlestown, MA 02129
Phone: 617-726-6211
Fax: 617-726-5760
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