Step 1 - Organise your data
Organise your data (bids compatible format) either in Project > Group > Subject > Modalities
Or as Project > Subject > Modalities
Fill out the template spreadsheet (download below). Make sure the project_name and root_folder are exactly the same as the Experiment and Subject folder names you used when organising the data. Also make sure subj_id is matches root_folder excluding the "sub-" prefix.
Step 2 - Create Project
Once logged-in, click on
Fill out project details
Enter project name (has to match exactly the project folder name and the project_name on the spreadsheet)
Write a brief project description
Enter project date and select species
Enter target group size (optional)
Add any number of attachments, including regressors if your project includes fMRI.
Add as many search terms as modalities in your project. All projects require an anatomical reference scan (Anat). Any number of TBM (Morph), rsMRI (Rest), fMRI (Func) and CBF (Perf) can be included. The search term should start with the modality folder (eg "anat/", "func/", etc) and then a search term that is unique to each run (eg "*T2w.nii.gz" or "*bold.nii.gz").
Add names of experimental groups. These should match exactly the exp_group names on the spreadsheet.
Once all information is entered, and you reviewed your search and group lists, click on
Step 3 - Upload data
Single Upload: Select the subject folder and enter relevant information; Make sure to select the correct Project (Study) and corresponding experimental Group (the rest of the information is optional)
Multi-upload: Select the spreadsheet you saved on Step 1 and then select the root folder (Project) where all the subjects are saved.
Once all files are selected, information is entered, and you reviewed te info, click on
You can follow the progress of the pre-processing work in the "Project Overview" page (go to Projects and click on the desired project's "Access Project" button). Once pre-processing is successfully finished a badge will show in the "Processed" column of the corresponding subject.
Step 4 - Review pre-processing
Review all subjects to "Accept" or "Reject" the data. Use the modalities drop-down to select each modality. You can use the left-right arrow keys to browse through subjects or use the subjects drop-down to choose a specific one. Click on the Accept/Reject dropdown once you are satisfied (or otherwise) the quality of the data is acceptable.
Step 5 - Setup stats
In the "Analysis" page you can setup statistical analysis which will only include the subjects accepted in Step 4.
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Use the modalities tabs to select the corresponding modality you want to analyse.
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Groups can be selected by clicking on the check boxes. For one-sample t-test (1STT), you can select several groups in one go. For two-sample (2STT) and paired t-tests (PTT) you should select only two groups.
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Use the "1st-2nd" drop-down to determine the direction of comparison (i.e. first group minus second or vice-versa; groups are numbered from top to the bottom of the list).
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Click "Add Test" to add the corresponding stats to the Stats list.
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Once all stats are defined, select the ones you want to submit to the queue (from the Stats list) by clicking on the corresponding check boxes.
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Click "Run Stats" to submit the stats to the server.
Suffixes in the group names represent the modality and the run number: R = resting state, P = CBF (perfusion), F = fMRI, M = TBM, followed by 1, 2, 3 etc for run-01, run-02, run-03 etc. The badges display the number of accepted subjects in each group.
You can follow the progress of the stats work in the "Project Overview" page (go to Projects and click on the desired project's "Access Project" button). Once stats processing is successfully finished a badge will show in the "Processed" column of the corresponding stats.
Step 6 - Review results
Once stats processing is successfully finished, results will be displayed in the "Results" page.
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Use the modalities tab to select the modality you want to explore (NBS and GT - graph theory - are only calculated for two-sample t-tes.
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Use the results drop-down to select the desired comparison.
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Table in Seed tab can be used to browser and sort results.
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Morph (TBM) tab shows voxel-wise and ROI (volume) results. A table with summary stats can be displayed by clicking on the icon; The bar graph is interactive and can be moved and zoomed.
