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[FIX] update demos #149

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Merged
merged 5 commits into from
Oct 31, 2020
Merged

[FIX] update demos #149

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da14a7b
update version.txt
Remi-Gau Oct 31, 2020
0714847
update demo 1168
Remi-Gau Oct 31, 2020
231c164
update demo ds 114
Remi-Gau Oct 31, 2020
637d36e
fix visMotion demo
Remi-Gau Oct 31, 2020
c26a079
mh fix
Remi-Gau Oct 31, 2020
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24 changes: 15 additions & 9 deletions demos/openneuro/ds000001_run.m
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Expand Up @@ -12,21 +12,27 @@
WD = fileparts(mfilename('fullpath'));

% we add all the subfunctions that are in the sub directories
addpath(fullfile(WD, '..'));
addpath(genpath(fullfile(WD, '..', 'src')));
addpath(genpath(fullfile(WD, '..', 'lib')));
addpath(genpath(fullfile(WD, '..', '..', 'src')));
addpath(genpath(fullfile(WD, '..', '..', 'lib')));

%% Set options
opt = ds000001_getOption();

checkDependencies();

%% Run batches
isMVPA = 0;
reportBIDS(opt);

bidsCopyRawFolder(opt, 1);

bidsSTC(opt);

% bidsCopyRawFolder(opt, 1);
bidsSpatialPrepro(opt);

anatomicalQA(opt);

bidsSmoothing(FWHM, opt);
% bidsFFX('specifyAndEstimate', opt, FWHM, isMVPA);
% bidsFFX('contrasts', opt, FWHM, isMVPA);
% bidsResults(opt, FWHM, [], isMVPA);

% Not implemented yet
% bidsFFX('specifyAndEstimate', opt, FWHM);
% bidsFFX('contrasts', opt, FWHM);
% bidsResults(opt, FWHM);
2 changes: 2 additions & 0 deletions demos/openneuro/ds000114_getOption.m
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Expand Up @@ -20,6 +20,8 @@
opt.anatReference.type = 'T1w';
opt.anatReference.session = 2;

opt.space = 'individual';

opt.model.file = fullfile(fileparts(mfilename('fullpath')), ...
'models', ...
'model-ds000114-linebisection_smdl.json');
Expand Down
18 changes: 6 additions & 12 deletions demos/openneuro/ds000114_run.m
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Expand Up @@ -12,27 +12,21 @@
WD = fileparts(mfilename('fullpath'));

% we add all the subfunctions that are in the sub directories
addpath(fullfile(WD, '..'));
addpath(genpath(fullfile(WD, '..', 'src')));
addpath(genpath(fullfile(WD, '..', 'lib')));
addpath(genpath(fullfile(WD, '..', '..', 'src')));
addpath(genpath(fullfile(WD, '..', '..', 'lib')));

%% Set options
opt = ds000114_getOption();

% the line below allows to run preprocessing in "native" space.
% - use realign and unwarp
% - don't do normalization
opt.space = 'individual';

checkDependencies();

%% Run batches

reportBIDS(opt);

bidsCopyRawFolder(opt, 1);

bidsSTC(opt);
% bidsCopyRawFolder(opt, 1);
%
% bidsSTC(opt);

bidsSpatialPrepro(opt);

Expand All @@ -44,4 +38,4 @@

bidsFFX('specifyAndEstimate', opt, FWHM);
bidsFFX('contrasts', opt, FWHM);
bidsResults(opt, FWHM, []);
bidsResults(opt, FWHM);
4 changes: 2 additions & 2 deletions demos/openneuro/ds001168_getOption.m
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Expand Up @@ -20,10 +20,10 @@
opt.anatReference.type = 'T1w';
opt.anatReference.session = 1;

opt.ignoreFieldmaps = false;
opt.space = 'individual';

%% DO NOT TOUCH
opt = checkOptions(opt);
% saveOptions(opt);
saveOptions(opt);

end
17 changes: 6 additions & 11 deletions demos/openneuro/ds001168_run.m
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Original file line number Diff line number Diff line change
Expand Up @@ -12,18 +12,12 @@
WD = fileparts(mfilename('fullpath'));

% we add all the subfunctions that are in the sub directories
addpath(fullfile(WD, '..'));
addpath(genpath(fullfile(WD, '..', 'src')));
addpath(genpath(fullfile(WD, '..', 'lib')));
addpath(genpath(fullfile(WD, '..', '..', 'src')));
addpath(genpath(fullfile(WD, '..', '..', 'lib')));

%% Set options
opt = ds001168_getOption();

% the line below allows to run preprocessing in "native" space.
% - use realign and unwarp
% - don't do normalization
opt.space = 'individual';

checkDependencies();

%% Run batches
Expand All @@ -41,9 +35,10 @@
anatomicalQA(opt);
bidsResliceTpmToFunc(opt);
functionalQA(opt);
%
% bidsSmoothing(FWHM, opt);
%

bidsSmoothing(FWHM, opt);

% Not implemented yet
% bidsFFX('specifyAndEstimate', opt, FWHM);
% bidsFFX('contrasts', opt, FWHM);
% bidsResults(opt, FWHM, []);
50 changes: 32 additions & 18 deletions demos/vismotion/batch.m
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Expand Up @@ -7,35 +7,49 @@
WD = fileparts(mfilename('fullpath'));

% we add all the subfunctions that are in the sub directories
addpath(fullfile(WD, '..'));
addpath(genpath(fullfile(WD, '..', 'src')));
addpath(genpath(fullfile(WD, '..', 'lib')));
addpath(genpath(fullfile(WD, '..', '..', 'src')));
addpath(genpath(fullfile(WD, '..', '..', 'lib')));

%% Run batches
opt = getOption();

checkDependencies();

% copy raw folder into derivatives folder
% BIDS_copyRawFolder(opt, 1)
reportBIDS(opt);

% preprocessing
% BIDS_STC(opt);
% BIDS_SpatialPrepro(opt);
% BIDS_Smoothing(6, opt);
bidsCopyRawFolder(opt, 1);
%
% % preprocessing
bidsSTC(opt);
bidsSpatialPrepro(opt);

% Quality control
anatomicalQA(opt);

% Not implemented yet
% bidsResliceTpmToFunc(opt);
% functionalQA(opt);

funcFWHM = 6;
bidsSmoothing(funcFWHM, opt);

% subject level Univariate
% BIDS_FFX(1, 6, opt);
% BIDS_FFX(2, 6, opt);
bidsFFX('specifyAndEstimate', opt, funcFWHM);
bidsFFX('contrasts', opt, funcFWHM);

% group level univariate
BIDS_RFX(1, 6, 6);
BIDS_RFX(2, 6, 6);
conFWHM = 6;
bidsRFX('smoothContrasts', funcFWHM, conFWHM, opt);

BIDS_Results(6, 6, opt, 0);
% Not implemented yet
% bidsRFX('RFX', funcFWHM, conFWHM, opt);

% Not implemented yet
% subject level multivariate
% isMVPA=1;
% BIDS_FFX(1, 6, opt, isMVPA);
% BIDS_FFX(2, 6, opt, isMVPA);
% make4Dmaps(6,opt)
% opt.model.file = fuufile(WD, ...
% 'models', ...
% 'model-motionDecodingMultivariate_smdl.json');
%
% bidsFFX('specifyAndEstimate', opt, funcFWHM);
% bidsFFX('contrasts', opt, funcFWHM);
% concatBetaImgTmaps(funcFWHM, opt);
5 changes: 3 additions & 2 deletions demos/vismotion/getOption.m
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Expand Up @@ -13,11 +13,12 @@
opt.taskName = 'visMotion';

% The directory where the data are located
opt.dataDir = '/home/remi/BIDS/visMotion/derivatives/';
opt.dataDir = '/home/remi/gin/CPP_visMotion/raw';
opt.derivativesDir = '/home/remi/Documents';

% specify the model file that contains the contrasts to compute
opt.model.file = ...
'/home/remi/github/CPP_BIDS_SPM_pipeline/model-visMotionLoc_smdl.json';
'/home/remi/github/CPP_BIDS_SPM_pipeline/demos/vismotion/models/model-visMotionLoc_smdl.json';

% specify the result to compute
% Contrasts.Name has to match one of the contrast defined in the model json file
Expand Down
26 changes: 17 additions & 9 deletions demos/vismotion/models/model-visMotionLoc_smdl.json
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Expand Up @@ -5,18 +5,22 @@
"task": "visMotion"
},
"Steps": [
{
"Level": "run",
"Model": {
"X": [
"trial_type.VisMot",
"trial_type.VisStat",
"trans_x", "trans_y", "trans_z", "rot_x", "rot_y", "rot_z"
]
}
},
{
"Level": "subject",
"Model": {
"X": [
"trial_type.Vis_U",
"trial_type.Vis_D",
"trial_type.Vis_R",
"trial_type.Vis_L",
"trial_type.Aud_U",
"trial_type.Aud_D",
"trial_type.Aud_L",
"trial_type.Aud_R",
"trial_type.VisMot",
"trial_type.VisStat",
"trans_x", "trans_y", "trans_z", "rot_x", "rot_y", "rot_z"
]
},
Expand All @@ -42,7 +46,11 @@
},
{
"Level": "dataset",
"AutoContrasts": ["trial_type.VisMot", "trial_type.VisStat", "VisMot_gt_VisStat", "VisStat_gt_VisMot"]
"AutoContrasts": [
"trial_type.VisMot",
"trial_type.VisStat",
"VisMot_gt_VisStat",
"VisStat_gt_VisMot"]
}
]
}
2 changes: 1 addition & 1 deletion version.txt
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
v0.0.3
v0.1.0