While trying to coregister a ct.nii and a orig.mgz file using the following command:
spmregister --s SUBJECT --mov ct.nii --reg spm.reg.dat --fsvol orig
I get the following error:
ERROR: spm_coreg
??? Undefined function or variable 'x'.
Finished after 0.023302 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
The SPM package used to work a few weeks ago. Did something change? Do I need to install something?
Thanks! Rodrigo
Can you send us the info requested in https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer?
doug
Rodrigo Zepeda wrote:
While trying to coregister a ct.nii and a orig.mgz file using the following command:
spmregister --s SUBJECT --mov ct.nii --reg spm.reg.dat --fsvol orig
I get the following error:
> ERROR: spm_coreg
??? Undefined function or variable 'x'.
Finished after 0.023302 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
The SPM package used to work a few weeks ago. Did something change? Do I need to install something?
Thanks! Rodrigo
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
I'm getting an error trying to coregister a ct.nii and a orig.mgz file.
The subjects directory is: /autofs/space/multnomah_002/users/Cashlab/BW10
Working directory: /autofs/space/multnomah_002/users/Cashlab/BW10/BW10_Pre_Op_MRI
"which spmregister" outputs this: /usr/local/freesurfer/stable4/bin/spmregister
I'm using the following command:
[multnomah:BW10_Pre_Op_MRI] (nmr-std-env) spmregister --s BW10_Pre_Op_MRI --mov ct.nii --reg spm.reg.dat --fsvol orig
I get the following error:
ERROR: spm_coreg
??? Undefined function or variable 'x'.
Finished after 0.023302 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
My environment information is:
-------- freesurfer-Linux-centos4-stable-v4.3.0-20090516 -------- 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/sake/3/users/inverse/subjects MNI_DIR /usr/local/freesurfer/stable4/mni FSL_DIR /usr/pubsw/packages/fsl/current
The SPM package used to work a few weeks ago. Did something change?
Thanks! Rodrigo
looks like you need to have spm in your matlab path. Try adding
path(path,'/usr/pubsw/common/spm/spm5');
in your ~/matlab/startup.m file
doug
Rodrigo Zepeda wrote:
Hi,
I'm getting an error trying to coregister a ct.nii and a orig.mgz file.
The subjects directory is: /autofs/space/multnomah_002/users/Cashlab/BW10
Working directory: /autofs/space/multnomah_002/users/Cashlab/BW10/BW10_Pre_Op_MRI
"which spmregister" outputs this: /usr/local/freesurfer/stable4/bin/spmregister
I'm using the following command:
[multnomah:BW10_Pre_Op_MRI] (nmr-std-env) spmregister --s BW10_Pre_Op_MRI --mov ct.nii --reg spm.reg.dat --fsvol orig
I get the following error:
> ERROR: spm_coreg
??? Undefined function or variable 'x'.
Finished after 0.023302 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
My environment information is:
-------- freesurfer-Linux-centos4-stable-v4.3.0-20090516 -------- 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/sake/3/users/inverse/subjects MNI_DIR /usr/local/freesurfer/stable4/mni FSL_DIR /usr/pubsw/packages/fsl/current
The SPM package used to work a few weeks ago. Did something change?
Thanks! Rodrigo
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
btw, you'll probably also need to have this env variable set too:
setenv FS_SPMREG_MATLAB /usr/pubsw/common/matlab/7.1/bin/matlab
Douglas N Greve wrote:
looks like you need to have spm in your matlab path. Try adding
path(path,'/usr/pubsw/common/spm/spm5');
in your ~/matlab/startup.m file
doug
Rodrigo Zepeda wrote:
Hi,
I'm getting an error trying to coregister a ct.nii and a orig.mgz file. The subjects directory is: /autofs/space/multnomah_002/users/Cashlab/BW10
Working directory: /autofs/space/multnomah_002/users/Cashlab/BW10/BW10_Pre_Op_MRI
"which spmregister" outputs this: /usr/local/freesurfer/stable4/bin/spmregister
I'm using the following command:
[multnomah:BW10_Pre_Op_MRI] (nmr-std-env) spmregister --s BW10_Pre_Op_MRI --mov ct.nii --reg spm.reg.dat --fsvol orig
I get the following error:
>> ERROR: spm_coreg
??? Undefined function or variable 'x'.
Finished after 0.023302 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
My environment information is:
-------- freesurfer-Linux-centos4-stable-v4.3.0-20090516 -------- 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/sake/3/users/inverse/subjects MNI_DIR /usr/local/freesurfer/stable4/mni FSL_DIR /usr/pubsw/packages/fsl/current
The SPM package used to work a few weeks ago. Did something change?
Thanks! Rodrigo
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Rodrigo Zepeda