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add print function to Mapping
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‎docs/source/index.rst‎

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@@ -9,3 +9,4 @@ Welcome to spm_2_bids documentation!
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general_information
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function_details
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mapping

‎docs/source/mapping.md‎

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<!--
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THIS FILE IS AUTOMATICALLY GENERATED!
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DO NOT EDIT MANUALLY!
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-->
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# Mapping
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| input | output |
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| - | - |
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| m\*.\* | \*space-individual_desc-biascor_\*.\* |
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| c1\*.\* | \*space-individual_label-GM_probseg.\* |
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| c2\*.\* | \*space-individual_label-WM_probseg.\* |
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| c3\*.\* | \*space-individual_label-CSF_probseg.\* |
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| iy_\*.\* | \*from-IXI549Space_to-T1w_mode-image_xfm.\* |
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| y_\*.\* | \*from-T1w_to-IXI549Space_mode-image_xfm.\* |
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| segparam_\*.\* | \*segparam.\* |
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| a\*.\* | \*space-individual_desc-stc_\*.\* |
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| au\*.\* | \*space-individual_desc-stc_\*.\* |
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| unwarpparam_\*.\* | \*unwarpparam.\* |
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| u\*.\* | \*space-individual_desc-realignUnwarp_\*.\* |
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| ua\*.\* | \*space-individual_desc-realignUnwarp_\*.\* |
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| rp_\*.\* | \*motion.tsv |
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| rp_a\*.\* | \*motion.tsv |
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| rp_au\*.\* | \*motion.tsv |
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| wc1\*.\* | \*space-IXI549Space_label-GM_probseg.\* |
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| wc2\*.\* | \*space-IXI549Space_label-WM_probseg.\* |
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| wc3\*.\* | \*space-IXI549Space_label-CSF_probseg.\* |
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| s\*.\* | \*space-individual_desc-smth_\*.\* |
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| sua\*.\* | \*space-individual_desc-smth_\*.\* |
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| sau\*.\* | \*space-individual_desc-smth_\*.\* |
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| sra\*.\* | \*space-individual_desc-smth_\*.\* |
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| su\*.\* | \*space-individual_desc-smth_\*.\* |
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| sr\*.\* | \*space-individual_desc-smth_\*.\* |
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| sw\*.\* | \*space-IXI549Space_desc-smth_\*.\* |
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| swua\*.\* | \*space-IXI549Space_desc-smth_\*.\* |
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| swau\*.\* | \*space-IXI549Space_desc-smth_\*.\* |
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| swra\*.\* | \*space-IXI549Space_desc-smth_\*.\* |
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| swu\*.\* | \*space-IXI549Space_desc-smth_\*.\* |
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| swr\*.\* | \*space-IXI549Space_desc-smth_\*.\* |
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| w\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
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| wm\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
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| wau\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
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| wua\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
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| wra\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
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| wu\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
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| wr\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
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| mean\*.\* | \*space-individual_desc-mean_\*.\* |
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| meanu\*.\* | \*space-individual_desc-mean_\*.\* |
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| meanua\*.\* | \*space-individual_desc-mean_\*.\* |
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| meanau\*.\* | \*space-individual_desc-mean_\*.\* |
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| wmeanu\*.\* | \*space-IXI549Space_desc-mean_\*.\* |
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| wmeanua\*.\* | \*space-IXI549Space_desc-mean_\*.\* |
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| wmeanau\*.\* | \*space-IXI549Space_desc-mean_\*.\* |
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‎src/defaults/Mapping.m‎

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@@ -159,52 +159,96 @@
159159

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end
161161

162-
function print_mapping(obj)
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function print_mapping(obj, filename)
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%
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% Print to screen by default.
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% Otherwise can print to a file (markdown) or a json
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%
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%
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% USAGE::
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%
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% map = print_mapping(filename)
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%
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164173
obj = flatten_mapping(obj);
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166-
fprintf(1, '\n');
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% print to screen be default;
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output_is_json = false;
167177

168-
for i = 1:size(obj.mapping, 1)
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% what to separate input and output with
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left = ' ';
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separator = ' --> ';
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right = ' ';
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170-
input = obj.mapping(i);
183+
if nargin < 2
171184

172-
if isfield(input, 'suffix') && isempty(input.suffix) || ...
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~isfield(input, 'suffix')
174-
input.suffix = '*';
175-
end
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fid = 1;
176186

177-
if isfield(input, 'ext') && ~isempty(input.ext)
178-
input.extension = '.*';
179-
end
180-
if ~isfield(input, 'extension') || isempty(input.extension)
181-
input.extension = '.*';
187+
elseif ~strcmp(spm_file(filename, 'ext'), 'json')
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fid = fopen(filename, 'Wt');
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if fid == -1
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error('Unable to write file %s.', filename);
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end
183193

184-
input = bids.File(input);
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left = '| ';
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separator = ' | ';
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right = ' |';
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186-
output = obj.mapping(i).name_spec;
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elseif strcmp(spm_file(filename, 'ext'), 'json')
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188-
if isfield(output, 'suffix') && isempty(output.suffix) || ...
189-
~isfield(output, 'suffix')
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output.suffix = '*';
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end
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output_is_json = true;
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193-
if isfield(output, 'ext') && ~isempty(output.ext)
194-
output.extension = '.*';
195-
end
196-
if ~isfield(output, 'extension') || isempty(output.extension)
197-
output.extension = '.*';
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else
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204+
fid = 1;
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end
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208+
header = ['<!--\n', ...
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' THIS FILE IS AUTOMATICALLY GENERATED!\n', ...
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' DO NOT EDIT MANUALLY!\n', ...
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'-->\n', ...
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'# Mapping\n\n', ...
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left, 'input', separator, 'output', right, '\n', ...
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left, '-', separator, '-', right, '\n'];
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if ~output_is_json
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fprintf(fid, '\n');
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if fid ~= 1
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fprintf(fid, header);
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end
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end
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for i = 1:size(obj.mapping, 1)
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if ~output_is_json
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%%
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input = obj.mapping(i);
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input = prepare_for_printing(input);
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%%
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output = obj.mapping(i).name_spec;
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output = prepare_for_printing(output);
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200-
output = bids.File(output);
201-
output.re;
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output.filename = ['*' output.filename];
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203-
fprintf(1, [input.filename ' --> ' output.filename '\n']);
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if fid ~= 1
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input.filename = strrep(input.filename, '*', '\*');
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output.filename = strrep(output.filename, '*', '\*');
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end
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240+
fprintf(fid, '%s%s%s%s%s\n', ...
241+
left, input.filename, separator, output.filename, right);
242+
end
204243

205244
end
206245

207-
fprintf(1, '\n');
246+
if ~output_is_json
247+
fprintf(fid, '\n');
248+
if fid ~= 1
249+
fclose(fid);
250+
end
251+
end
208252

209253
end
210254

@@ -310,3 +354,20 @@ function print_mapping(obj)
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311355
end
312356
end
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function bf = prepare_for_printing(spec)
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360+
if isfield(spec, 'suffix') && isempty(spec.suffix) || ...
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~isfield(spec, 'suffix')
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spec.suffix = '*';
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end
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365+
if isfield(spec, 'ext') && ~isempty(spec.ext)
366+
spec.extension = '.*';
367+
end
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if ~isfield(spec, 'extension') || isempty(spec.extension)
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spec.ext = '.*';
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end
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372+
bf = bids.File(spec);
373+
end

‎src/defaults/check_cfg.m‎

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@@ -105,8 +105,7 @@
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'suffix', 'probseg');
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107107
% Segmentation output
108-
segment.bias_corrected = struct('entities', struct('desc', 'biascor', ...
109-
'space', 'individual'));
108+
segment.bias_corrected = desc_gen('biascor');
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111110
segment.gm = segment_gen('GM');
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segment.wm = segment_gen('WM');

‎tests/mapping.md‎

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<!--
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THIS FILE IS AUTOMATICALLY GENERATED!
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DO NOT EDIT MANUALLY!
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-->
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# Mapping
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| input | output |
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| - | - |
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| m\*.\* | \*space-individual_desc-biascor_\*.\* |
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| c1\*.\* | \*space-individual_label-GM_probseg.\* |
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| c2\*.\* | \*space-individual_label-WM_probseg.\* |
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| c3\*.\* | \*space-individual_label-CSF_probseg.\* |
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| iy_\*.\* | \*from-IXI549Space_to-T1w_mode-image_xfm.\* |
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| y_\*.\* | \*from-T1w_to-IXI549Space_mode-image_xfm.\* |
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| segparam_\*.\* | \*segparam.\* |
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| a\*.\* | \*space-individual_desc-stc_\*.\* |
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| au\*.\* | \*space-individual_desc-stc_\*.\* |
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| unwarpparam_\*.\* | \*unwarpparam.\* |
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| u\*.\* | \*space-individual_desc-realignUnwarp_\*.\* |
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| ua\*.\* | \*space-individual_desc-realignUnwarp_\*.\* |
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| rp_\*.\* | \*motion.tsv |
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| rp_a\*.\* | \*motion.tsv |
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| rp_au\*.\* | \*motion.tsv |
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| wc1\*.\* | \*space-IXI549Space_label-GM_probseg.\* |
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| wc2\*.\* | \*space-IXI549Space_label-WM_probseg.\* |
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| wc3\*.\* | \*space-IXI549Space_label-CSF_probseg.\* |
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| s\*.\* | \*space-individual_desc-smth_\*.\* |
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| sua\*.\* | \*space-individual_desc-smth_\*.\* |
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| sau\*.\* | \*space-individual_desc-smth_\*.\* |
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| sra\*.\* | \*space-individual_desc-smth_\*.\* |
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| su\*.\* | \*space-individual_desc-smth_\*.\* |
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| sr\*.\* | \*space-individual_desc-smth_\*.\* |
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| sw\*.\* | \*space-IXI549Space_desc-smth_\*.\* |
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| swua\*.\* | \*space-IXI549Space_desc-smth_\*.\* |
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| swau\*.\* | \*space-IXI549Space_desc-smth_\*.\* |
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| swra\*.\* | \*space-IXI549Space_desc-smth_\*.\* |
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| swu\*.\* | \*space-IXI549Space_desc-smth_\*.\* |
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| swr\*.\* | \*space-IXI549Space_desc-smth_\*.\* |
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| w\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
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| wm\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
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| wau\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
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| wua\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
44+
| wra\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
45+
| wu\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
46+
| wr\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
47+
| mean\*.\* | \*space-individual_desc-mean_\*.\* |
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| meanu\*.\* | \*space-individual_desc-mean_\*.\* |
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| meanua\*.\* | \*space-individual_desc-mean_\*.\* |
50+
| meanau\*.\* | \*space-individual_desc-mean_\*.\* |
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| wmeanu\*.\* | \*space-IXI549Space_desc-mean_\*.\* |
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| wmeanua\*.\* | \*space-IXI549Space_desc-mean_\*.\* |
53+
| wmeanau\*.\* | \*space-IXI549Space_desc-mean_\*.\* |
54+

‎tests/test_mapping_print.m‎

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Original file line numberDiff line numberDiff line change
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1+
% (C) Copyright 2021 spm_2_bids developers
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function test_suite = test_mapping_print %#ok<*STOUT>
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try % assignment of 'localfunctions' is necessary in Matlab >= 2016
5+
test_functions = localfunctions(); %#ok<*NASGU>
6+
catch % no problem; early Matlab versions can use initTestSuite fine
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end
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initTestSuite;
9+
end
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11+
function test_mapping_print_basic()
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13+
map = Mapping();
14+
map = map.default();
15+
map.print_mapping();
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17+
map.print_mapping(fullfile('mapping.md'));
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19+
end

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