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--- processing_stream_-_image_file_conversion [2010/05/26 17:23] – added the depth argument to findfiles 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)
     % take out those which match the CHIP* part
-    [study, chip] = fileparts(fileparts(donedirs{dc}));
+    [study, chip] = fileparts(fileparts(fileparts(donedirs{dc})));
     importdirs(~isemptycell(regexp(importdirs, chip))) = [];
 end
@@ Line 49: / Line 56: @@
     % find dicom files
-    dcmfiles = findfiles(importdirs{dc}, '*.dcm');
+    dcmfiles = findfiles(importdirs{dc}, '*.dcm', 'depth=1');
     % no files, continue
@@ Line 58: / Line 65: @@
     % figure out the target folder
     [study, target] = fileparts(fileparts(dcmfiles{1}));
+    % re-vamp the target folder name (which for us is NUMVOLr_NUMSCAN)
+    target_particles = regexp(target, '^(\d+)r_(\d+)$', 'tokens');
+    if isempty(target_particles) || ...
+        numel(target_particles{1}) ~= 2
+        continue;
+    end
+    target = sprintf('r%02d_%03d', ...
+        str2double(target_particles{1}{2}), ...
+        str2double(target_particles{1}{1}));
     % create target folder
-    target = [fileparts(study) '/run_' target];
+    target = [fileparts(study) '/func/' target];
     mkadir(target);
@@ Line 66: / 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