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processing_stream_-_image_file_conversion [2010/05/26 19:35]
jochen Yet another correction for the search folders...
processing_stream_-_image_file_conversion [2010/05/30 05:36] (current)
jochen added instructions for SPM8
Line 21: Line 21:
 To ensure that the sorted list of filenames to be imported are in a correct temporal order, the use of the [[renamedicom]] function is highly recommended (unless you can confirm that the files you have already are properly named). To ensure that the sorted list of filenames to be imported are in a correct temporal order, the use of the [[renamedicom]] function is highly recommended (unless you can confirm that the files you have already are properly named).
  
-This functionality is **not yet** available as a compound function, but can be easily achieved by using the following code (adapted to your specific situation, of course):+This functionality is **not yet** available as a compound function, but can be easily achieved by using the following code for SPM5 (adapted to your specific situation, of course; wherever necessary and SPM8 instructions require, this is marked!):
  
 <code matlab>% load the DICOM import job file <code matlab>% load the DICOM import job file
 jobs = neuroelf_file('​p',​ '​spm5_dicomimport_job'​);​ jobs = neuroelf_file('​p',​ '​spm5_dicomimport_job'​);​
 +% for SPM8 it's '​spm8_dicomimport_job'​ of course!
 jobs = jobs.jobs; jobs = jobs.jobs;
  
 % use SPM's defaults % use SPM's defaults
-spm_defaults;​ % for SPM8 use spm('​defaults',​ '​FMRI'​);​+spm_defaults;​ 
 +% for SPM8 use spm('​defaults',​ '​FMRI'​);​ 
 + 
 +% ** IF YOU WISH TO USE THE SINGLE-FILE NIFTI FORMAT, SAY 
 +% jobs{1}.util{1}.dicom.convopts.format = '​nii';​ % for SPM5 or 
 +% jobs{1}.spm.util.dicom.convopts.format = '​nii';​ % for SPM8 ! 
 +% ** OTHERWISE THE TWO-FILE HDR+IMG FORMAT IS USED! **
  
 % change into your study'​s folder % change into your study'​s folder
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     jobs{1}.util{1}.dicom.data = dcmfiles;     jobs{1}.util{1}.dicom.data = dcmfiles;
     jobs{1}.util{1}.dicom.outdir{1} = target;     jobs{1}.util{1}.dicom.outdir{1} = target;
 +    % for SPM8, these two lines must be
 +    % jobs{1}.spm.util.dicom.data = dcmfiles;
 +    % jobs{1}.spm.util.dicom.outdir{1} = target;
     ​     ​
     % run import job     % run import job
processing_stream_-_image_file_conversion.txt · Last modified: 2010/05/30 05:36 by jochen