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--- processing_stream_-_image_file_conversion [2010/05/26 17:34] – Corrected the target path, etc. jochen
+++ processing_stream_-_image_file_conversion [2010/05/30 03:36] (current) – added instructions for SPM8 jochen
@@ 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).
-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
 jobs = neuroelf_file('p', 'spm5_dicomimport_job');
+% for SPM8 it's 'spm8_dicomimport_job' of course!
 jobs = jobs.jobs;
 % 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
@@ Line 34: / Line 41: @@
 % find all folders that contain DICOM import files (sessions)
-importdirs = findfiles([pwd '/CHIP*/func/raw'], '*', 'dirs=1', 'depth=1');
+importdirs = findfiles([pwd '/CHIP*/raw'], '*r*', 'dirs=1', 'depth=1');
 % remove subjects that have already been imported
-donedirs = findfiles([pwd '/CHIP*/func'], 'run*', 'dirs=1', 'depth=1');
+donedirs = findfiles([pwd '/CHIP*/func'], 'r*', 'dirs=1', 'depth=1');
 for dc = 1:numel(donedirs)
@@ Line 76: / Line 83: @@
     jobs{1}.util{1}.dicom.data = dcmfiles;
     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