Hi,

thanks, the job-transversion seems to work now. At least the job-descriptions looks different (jobs{1,1}{1,1}.spm.spatial.realign.estwrite... instead of jobs{1,1}.spatial{1,1}.realign{1,1}.estwrite..)

But wenn running the job I still get an error message:

Item 'Session', field 'val': Value must be either empty, a cellstr or a cfg_dep object.

-----------------------------------------------------------------------

Running job #4

-----------------------------------------------------------------------
No executable modules, but still unresolved dependencies or incomplete module inputs.
The following modules did not run:
Skipped: Realign: Estimate & Reslice

??? Error using ==> cfg_util>local_runcj at 1426
Job execution failed. The full log of this run can be found in
MATLAB command window, starting with the lines (look for the line
showing the exact #job as displayed in this error message)
------------------

Running job #4

------------------
Error in ==> cfg_util at 699

Error in ==> spm_jobman at 207
Error in ==> TransformationToMNI_spm8 at 251


So maybe the job-description is still not correct? The error message does say a lot, so I don't really no where so problem is.

Best wishes
Corinna



Zitat von YAN Chao-Gan <[log in to unmask]>:

Hi!
      Sorry, I said it too concisely.

       if SPMversion==5
           spm_jobman('run',jobs);
       elseif SPMversion==8  %YAN Chao-Gan, 090925. SPM8 compatible.
           jobs = spm_jobman('spm5tospm8',{jobs});
           spm_jobman('run',jobs{1});
       else
           uiwait(msgbox('The current SPM version is not supported by
DPARSF. Please install SPM5 or SPM8 first.','Invalid SPM Version.'));
           return
       end



     I think now you know how to use it.
     Best wishes!
                                                   Chao-Gan

On Tue, Oct 27, 2009 at 5:29 PM, <[log in to unmask]>wrote:

Hi,
thanks for the tip, but somehow it doesn't work. I get an error  message
during the 'spm5tospm8' transversion:

??? Cell contents reference from a non-cell array object.

Error in ==> spm_jobman>canonicalise_job at 274
      comp(cj) = comp(cj) && any(strcmp(fieldnames(job{cj}{k}), ...

Error in ==> spm_jobman at 214
          varargout{1} = canonicalise_job(varargin{2});

Error in ==> TransformAnatomyToMNI_spm8 at 114
      job = spm_jobman('spm5tospm8',jobs);

I don't know if my 'job'-description is wrong. I've attached it exported as
a mat-file (for the realignment and the estimation (segment-job)).
Hope you have an idea, of how to solve this problem.

Best wishes
Corinna


Zitat von YAN Chao-Gan <[log in to unmask]>:


 Hi!

 You may need to do job = spm_jobman('spm5tospm8',jobs) first.
  Best wishes!
                             Chao-Gan

On Tue, Oct 27, 2009 at 1:15 AM, Corinna Vehlow <
[log in to unmask]> wrote:

 Hi,

I have written a matlab script that performs all the spatial processing
steps after each other, starting with realignment, over coregistration,
estimation of the transformation warp and finally normalisation. We used
the
script to transform anatomical and functional brain data into MNI space.
The
script was written to run with spm5. Now we switched to spm8 and I get
the
following output/mistake in Matlab during the Realignment method (the
Dicom
conversion works correct):

Item 'Session', field 'val': Value must be either empty, a cellstr or a
cfg_dep object.

-----------------------------------------------------------------------
Running job #7
-----------------------------------------------------------------------
No executable modules, but still unresolved dependencies or incomplete
module inputs.
The following modules did not run:
Skipped: Realign: Estimate & Reslice

??? Error using ==> cfg_util>local_runcj at 1426
Job execution failed. The full log of this run can be found in MATLAB
command
window, starting with the lines (look for the line showing the exact #job
as
displayed in this error message)
------------------
Running job #7
------------------

Error in ==> cfg_util at 699

Error in ==> spm_jobman at 203

Error in ==> TransformationToMNI_spm8 at 225

Do I have to start the jobroutines differently under spm8, in comparison
to
spm5?
Does anybody know how to run those tasks/jobs with spm8?

I run the job with the command:
spm_jobman('run',jobs)

where jobs is of form:
jobs{1}.spatial{1}.realign{1}.estwrite.eoptions
...eoptions.quality = 1
...eoptions.sep = 3
...eoptions.fwhm = 5
...eoptions.rtm = 1
...eoptions.interp = 7
...eoptions.wrap = [0,0,0]
...eoptions.weight = <0x0cell>
jobs{1}.spatial{1}.realign{1}.estwrite.roptions
...roptions.which = [0,1]
...roptions.interp = 7
...roptions.wrap = [0,0,0]
...roptions.mask = 1
jobs{1}.spatial{1}.realign{1}.estwrite.data


Hope someone can help! Thanks a lot!

Best wishes
Corinna