diff --git a/.gitignore b/.gitignore index ee62923..aa93884 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,7 @@ +folders + poster_ohbm_2023_bidspm.pdf poster/betterposter-template* -# General .DS_Store diff --git a/README.md b/README.md index 926871d..984297e 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,5 @@ + +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8099835.svg)](https://doi.org/10.5281/zenodo.8099835) [![License: CC BY 3.0](https://img.shields.io/badge/License-CC_BY_3.0-lightgrey.svg)](https://creativecommons.org/licenses/by/3.0/) -# Poster for bidspm for OHBM 2023 \ No newline at end of file +# Poster for bidspm for OHBM 2023 diff --git a/poster/docker.sh b/poster/docker.sh new file mode 100644 index 0000000..afde046 --- /dev/null +++ b/poster/docker.sh @@ -0,0 +1,12 @@ +docker run -it --rm \ + -v $sourcedata:/sourcedata \ + -v $derivatives:/derivatives \ + -v $model_dir:/models \ + cpplab/bidspm:latest \ + /sourcedata/raw \ + /derivatives \ + subject \ + --action stats \ + --preproc_dir /derivatives/bidspm-preproc \ + --model_file /models/smdl.json \ + --fwhm 6 diff --git a/poster/icons/iconmonstr-checkbox-19.svg b/poster/icons/iconmonstr-checkbox-19.svg new file mode 100644 index 0000000..818623d --- /dev/null +++ b/poster/icons/iconmonstr-checkbox-19.svg @@ -0,0 +1 @@ + diff --git a/poster/icons/iconmonstr-folder-thin.svg b/poster/icons/iconmonstr-folder-thin.svg new file mode 100644 index 0000000..446e1ce --- /dev/null +++ b/poster/icons/iconmonstr-folder-thin.svg @@ -0,0 +1 @@ + diff --git a/poster/images/qr-code.png b/poster/images/qr-code.png index 2d695d9..2a4aea3 100644 Binary files a/poster/images/qr-code.png and b/poster/images/qr-code.png differ diff --git a/poster/inputs.txt b/poster/inputs.txt new file mode 100644 index 0000000..bd12956 --- /dev/null +++ b/poster/inputs.txt @@ -0,0 +1,7 @@ +├── sourcedata +│ ├── fmriprep +│ └── raw +├── derivatives +│ └── bidspm-preproc +└── models + └── smdl.json diff --git a/poster/matlab.m b/poster/matlab.m new file mode 100644 index 0000000..623e0be --- /dev/null +++ b/poster/matlab.m @@ -0,0 +1,20 @@ +%% smooth +bidspm(fmriprep_dir, ... + derivatives, ... + 'subject', ... + 'action', 'smooth', ... + 'task', {'Motion'}, 'space', ... + {'MNI152NLin6Asym'}, 'fwhm', 6); + +%% stat +bidspm(bids_dir, derivatives, 'subject', + 'action', 'stats', ... + 'preproc_dir', preproc_dir, + 'model_file', model_file, ... + 'fwhm', 6); + +bidspm(bids_dir, derivatives, 'dataset', + 'action', 'stats', ... + 'preproc_dir', preproc_dir, + 'model_file', model_file, ... + 'fwhm', 6); diff --git a/poster/output.txt b/poster/output.txt index 8884fe0..060f05d 100644 --- a/poster/output.txt +++ b/poster/output.txt @@ -1,4 +1,3 @@ -. ├── sub-01 │   └── task-Motion_space-MNI152NLin6Asym_FWHM-6 │   ├── SPM.mat diff --git a/poster/poster_ohbm_2023_bidspm.svg b/poster/poster_ohbm_2023_bidspm.svg index 499b2d7..1e0079b 100644 --- a/poster/poster_ohbm_2023_bidspm.svg +++ b/poster/poster_ohbm_2023_bidspm.svg @@ -19,6 +19,31 @@ xmlns:cc="http://creativecommons.org/ns#" xmlns:dc="http://purl.org/dc/elements/1.1/">.cls-1{fill:#1a1a1a;}.cls-1{fill:#1a1a1a;}image/svg+xmlRemi Gau1, Marco Barilari1, Ceren Battal1, Jeanne Caron-Guyon1, Filippo Cerpelloni1,2, Federica Falagiarda1, Michèle MacLean3, Stefania Mattioni4, Mohamed Rezk1, Iqra Shahzad1, Ying Yang1, Olivier Collignon11 - Institute for research in Psychology (IPSY) & + Neuroscience (IoNS), UCLouvain, Louvain la Neuve, Belgium +2 - Brain and cognition, Leuven Brain Institute, KU Leuven, Leuven, Belgium +3 - Département de psychologie, Université de Montréal, Montréal, Canada +4 - ExperimentalPsychology, Ghent University, Ghent, BelgiumDOIDOI10.5281/zenodo.8099835Scan for the latest version of the posterRun all your fMRI univariate analysis with one JSON file and 50 lines of code.Dark primary#303f9f + id="tspan17496">Dark primary#303f9f Light primary color#c5cae9 + id="tspan17500">Light primary color#c5cae9 Primary color#3f51b5 + id="tspan17504">Primary color#3f51b5 Text / Icons#FFFFFF + id="tspan17508">Text / Icons#FFFFFF Accent color#03a9f4 + id="tspan17512">Accent color#03a9f4 Primary text#212121 + id="tspan17516">Primary text#212121 Secondary text#757575 + id="tspan17520">Secondary text#757575 Divider color #BDBDBD{ - "Name": "auditory motion localizer analysis", - "BIDSModelVersion": "1.0.0", - "Input": {"task": ["Motion"], - "space": ["MNI152NLin6Asym"] - }, - "Nodes": [ - { "Level": "Run", - "Name": "run_level", - "GroupBy": ["run", "subject"], - "Model": {"X": ["Motion", "Static", "trans_?", "rot_?"], - "HRF": {"Variables": ["Motion", "Static"], - "Model": "spm"}, - "Type": "glm"}, - "Contrasts": [{ "Name": "Motion_gt_Static", - "ConditionList": ["Motion", "Static"], - "Weights": [1 , -1 ], - "Test": "t"}] - }, - { "Level": "Subject", - "Name": "subject_level", - "GroupBy": ["contrast", "subject"], - "Model": {"X": [1], "Type": "glm"}, - "DummyContrasts": {"Test": "t"}}, - { "Level": "Dataset", - "Name": "within_group", - "GroupBy": ["contrast", "group"], - "Model": {"X": [1], - "Type": "glm", - "Software": {"bidspm": {"Results": [{ "name": ["Motion_gt_Static"], - "MC": "FWE", - "p": 0.05, - "k": 10, - "nidm": true}]}}}, - "DummyContrasts": {"Test": "t"}}, - { "Level": "Dataset", - "Name": "between_groups", - "GroupBy": ["contrast"], - "Model": {"Type": "glm", - "X": [1, "group"]}, - "Contrasts": [{ "Name": "blind_gt_control", - "ConditionList": ["group.blind", "group.control"], - "Weights": [1, -1 ], - "Test": "t"}]} - ], - "Edges": [ - {"Source": "run_level", "Destination": "subject_level"}, - {"Source": "subject_level", "Destination": "between_groups"}, - {"Source": "subject_level", "Destination": "within_group"} - ] -} -Divider color #BDBDBDFeaturesStandardized inputs- standardized inputs - - BIDS raw data - - BIDS derivatives data - - BIDS statistical model -- standarized API - - BIDS app -- standardized outputs - - NIDM results -- mass univariate or ROI -- octave compatibleStandardized outputsBIDS app APIbidspm: an SPM centric appbidspm: an SPM centric app├── derivatives -│   └── bidspm-groupStats -│   ├── sub-control_task-Motion_space-MNI152NLin6Asym_FWHM-6_contrast-MotionGtStatic -│   │   ├── beta_*.nii -│   │   ├── con_*.nii -│   │   ├── spmT_*.nii -│   │   ├── *.nidm.zip -│   │   ├── spm_*.png -│   │   ├── spm_*.tsv -│   │   ├── SPM.mat -│   │   └── *_designmatrix.png -│   ├── sub-blind_task-Motion_space-MNI152NLin6Asym_FWHM-6_contrast-StaticGtMotion -│   └── sub-ALL_task-Motion_space-MNI152NLin6Asym_FWHM-6_contrast-StaticGtMotion -├── sub-control01 -│   └── task-Motion_space-MNI152NLin6Asym_FWHM-6 -│   ├── beta_*.nii -│   ├── con_*.nii -│   ├── spmT_*.nii -│   ├── spm_*.png -│   ├── spm_*.tsv -│   ├── SPM.mat -│   ├── sub-control01_ses-01_task-Motion_desc-confounds_timeseries.tsv -│   ├── sub-control01_ses-01_task-Motion_onsets.tsv -│   ├── sub-control01_*_designmatrix.png -│   └── sub-control01_*_p-0pt050_k-0_MC-FWE_montage.png -├── sub-control* -└── sub-blind*model_file = fullfile(root_dir, 'models', 'model-MotionLoc_smdl.json'); -input_dir = fullfile(root_dir, 'inputs'); -bids_dir = fullfile(input_dir, 'raw'); -fmriprep_dir = fullfile(input_dir, 'fmriprep'); -output_dir = fullfile(root_dir, 'outputs', 'derivatives'); -preproc_dir = fullfile(output_dir, 'bidspm-preproc'); - -bidspm(fmriprep_dir, output_dir, 'subject', ... - 'action', 'smooth', ... - 'task', {'Motion'}, ... - 'space', {'MNI152NLin6Asym'}, ... - 'fwhm', 6); - -bidspm(bids_dir, output_dir, 'subject', ... - 'action', 'stats', ... - 'preproc_dir', preproc_dir, ... - 'model_file', model_file); - -bidspm(bids_dir, output_dir, 'dataset', ... - 'action', 'stats', ... - 'preproc_dir', preproc_dir, ... - 'model_file', model_file); -DOIDOI10.5281/zenodo.743903510.5281/zenodo.7439035Scan to access the pdfRemi Gau1, Marco Barilari1, Ceren Battal1, Jeanne Caron-Guyon1, Filippo Cerpelloni1,2, Federica Falagiarda1, Michèle MacLean3, Stefania Mattioni4, Mohamed Rezk1, Iqra Shahzad1, Ying Yang1, Olivier Collignon1├── sub-01 +│   └── task-Motion_space-MNI152NLin6Asym_FWHM-6 +│   ├── SPM.mat +│   ├── spm_*.png +│   ├── spm_*.tsv +│   ├── sub-01_ses-01_task-Motion_desc-confounds_timeseries.tsv +│   ├── sub-01_ses-01_task-Motion_onsets.tsv +│   ├── sub-01_*_designmatrix.png +│   └── sub-01_*_p-0pt050_k-0_MC-FWE_montage.png +├── sub-* +└──derivatives +    └── bidspm-groupStats +    └── *_task-Motion_space-MNI152NLin6Asym_FWHM-6_contrast-MotionGtStatic +       ├── SPM.mat +       ├── spm_*.png +       ├── spm_*.tsv +       ├── *_designmatrix.png +       └── *.nidm.zip1 - Institute for research in Psychology (IPSY) & + transform="matrix(0.4487439,0,0,0.4487439,-12.220351,-299.24057)" + id="text7657" + style="font-size:16.509px;white-space:pre;shape-inside:url(#rect7659);display:inline;fill:#212121;fill-opacity:1;stroke:none;stroke-width:4.4;stroke-linejoin:bevel;paint-order:stroke fill markers">%% smooth Neuroscience (IoNS), UCLouvain, Louvain la Neuve, Belgium + x="117.29492" + y="2000.2361" + id="tspan17670">bidspm(fmriprep_dir, ... 2 - Brain and cognition, Leuven Brain Institute, KU Leuven, Leuven, Belgium + x="117.29492" + y="2021.0336" + id="tspan17674"> derivatives, ... 3 - Département de psychologie, Université de Montréal, Montréal, Canada + x="117.29492" + y="2041.8311" + id="tspan17678"> 'subject', ... 4 - ExperimentalPsychology, Ghent University, Ghent, Belgium 'action', 'smooth', ... + 'task', {'Motion'}, 'space', ... + {'MNI152NLin6Asym'}, 'fwhm', 6); + +%% stat +bidspm(bids_dir, derivatives, 'subject', + 'action', 'stats', ... + 'preproc_dir', preproc_dir, + 'model_file', model_file, ... + 'fwhm', 6); + +bidspm(bids_dir, derivatives, 'dataset', + 'action', 'stats', ... + 'preproc_dir', preproc_dir, + 'model_file', model_file, ... + 'fwhm', 6); +Run all your fMRI univariate analysis with one JSON file and 50 lines of code. + transform="matrix(0.59959603,0,0,0.59959603,-26.133103,-690.78964)" + id="text8407" + style="font-size:12.3555px;white-space:pre;shape-inside:url(#rect8409);display:inline;fill:#212121;fill-opacity:1;stroke:none;stroke-width:4.4;stroke-linejoin:bevel;paint-order:stroke fill markers">docker run -it --rm \ + -v $sourcedata:/sourcedata \ + -v $derivatives:/derivatives \ + -v $model_dir:/models \ + cpplab/bidspm:latest \ + /sourcedata/raw \ + /derivatives \ + subject \ + --action stats \ + --preproc_dir /derivatives/bidspm-preproc \ + --model_file /models/smdl.json \ + --fwhm 6├── sourcedata +│ ├── fmriprep +│ └── raw +├── derivatives +│ └── bidspm-preproc +└── models + └── smdl.json + diff --git a/poster/step_2_stats.m b/poster/step_2_stats.m deleted file mode 100644 index 487b8d9..0000000 --- a/poster/step_2_stats.m +++ /dev/null @@ -1,14 +0,0 @@ -%% smooth -bidspm(fmriprep_dir, ... - output_dir, ... - 'subject', ... - 'action', 'smooth', ... - 'task', {'Motion'}, 'space', ... - {'MNI152NLin6Asym'}, 'fwhm', 6); - -%% stat -bidspm(bids_dir, output_dir, 'subject', 'action', 'stats', ... - 'preproc_dir', preproc_dir, 'model_file', model_file, 'fwhm', 6); - -bidspm(bids_dir, output_dir, 'dataset', 'action', 'stats', ... - 'preproc_dir', preproc_dir, 'model_file', model_file, 'fwhm', 6); diff --git a/poster/zenodo.7439035.svg b/poster/zenodo.8099835.svg similarity index 93% rename from poster/zenodo.7439035.svg rename to poster/zenodo.8099835.svg index a20691d..c50a312 100644 --- a/poster/zenodo.7439035.svg +++ b/poster/zenodo.8099835.svg @@ -19,10 +19,10 @@ DOI - 10.5281/zenodo.7439035 + 10.5281/zenodo.8099835 - 10.5281/zenodo.7439035 + 10.5281/zenodo.8099835