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 whichworked 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
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 whichworked 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 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
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 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
freesurfer@nmr.mgh.harvard.edu
-
Chindhuri Selvadurai -
Douglas N Greve