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
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