# Outputs ## jobs and logs Each batch is saved in `jobs` folder in time a stamped m-file: those are more human readable and interoperable than their equivalent `.mat` file, and they can still be loaded in the SPM batch interface. It is accompanied by a `.json` file that contains information about the environment in which the batch was run (operating system, bidspm version...). ```text bidspm-stats ├── jobs │   └── taskName │   ├── sub-01 │ │ ├── batch_batchName_task-taskName_space-space_FWHM-0_YYYY-MM-HHTMM-SS.json │ │ └── batch_batchName_task_taskName_space_space_FWHM_0_YYYY-MM-HHTMM-SS.m │   ├── sub-02 ``` ## preprocessing For a complete list of how SPM outputs are renamed into BIDS derivatives see the [Mapping](mapping) page. ### func | SPM | BIDS | | ----------------------------------- | ----------------------------------------------------------- | | s6usub-01_task-auditory_bold.nii | sub-01_task-auditory_space-individual_desc-smth6_bold.nii | | s6rsub-01_task-auditory_bold.nii | sub-01_task-auditory_space-individual_desc-smth6_bold.nii | | s6uasub-01_task-auditory_bold.nii | sub-01_task-auditory_space-individual_desc-smth6_bold.nii | | s6rasub-01_task-auditory_bold.nii | sub-01_task-auditory_space-individual_desc-smth6_bold.nii | | s6wusub-01_task-auditory_bold.nii | sub-01_task-auditory_space-IXI549Space_desc-smth6_bold.nii | | s6wrsub-01_task-auditory_bold.nii | sub-01_task-auditory_space-IXI549Space_desc-smth6_bold.nii | | s6wuasub-01_task-auditory_bold.nii | sub-01_task-auditory_space-IXI549Space_desc-smth6_bold.nii | | s6wrasub-01_task-auditory_bold.nii | sub-01_task-auditory_space-IXI549Space_desc-smth6_bold.nii | | s6sub-01_task-auditory_bold.nii | sub-01_task-auditory_desc-smth6_bold.nii | | rp_sub-01_task-auditory_bold.txt | sub-01_task-auditory_desc-confounds_regressors.tsv | | rp_asub-01_task-auditory_bold.txt | sub-01_task-auditory_desc-confounds_regressors.tsv | | usub-01_task-auditory_bold.nii | sub-01_task-auditory_space-individual_desc-preproc_bold.nii | | uasub-01_task-auditory_bold.nii | sub-01_task-auditory_space-individual_desc-preproc_bold.nii | | rsub-01_task-auditory_bold.nii | sub-01_task-auditory_space-individual_desc-preproc_bold.nii | | rasub-01_task-auditory_bold.nii | sub-01_task-auditory_space-individual_desc-preproc_bold.nii | | std_usub-01_task-auditory_bold.nii | sub-01_task-auditory_space-individual_desc-std_bold.nii | | std_uasub-01_task-auditory_bold.nii | sub-01_task-auditory_space-individual_desc-std_bold.nii | ### anat ```{note} Not listed: - some of the outputs of the segmentation done by the ALI toolbox for lesion detection ``` | SPM | BIDS | | ------------------------------------------------------------ | ------------------------------------------------------- | | wc1sub-01_T1w.nii | sub-01_space-IXI549Space_res-bold_label-GM_probseg.nii | | wc2sub-01_T1w.nii | sub-01_space-IXI549Space_res-bold_label-WM_probseg.nii | | wc3sub-01_T1w.nii | sub-01_space-IXI549Space_res-bold_label-CSF_probseg.nii | | rc1sub-01_T1w.nii | sub-01_space-individual_res-bold_label-GM_probseg.nii | | rc2sub-01_T1w.nii | sub-01_space-individual_res-bold_label-WM_probseg.nii | | rc3sub-01_T1w.nii | sub-01_space-individual_res-bold_label-CSF_probseg.nii | | wmsub-01_T1w.nii | sub-01_space-IXI549Space_res-r1pt0_T1w.nii | | wmsub-01_desc-skullstripped_T1w.nii | sub-01_space-IXI549Space_res-r1pt0_desc-preproc_T1w.nii | | msub-01_desc-skullstripped_T1w.nii | sub-01_space-individual_desc-preproc_T1w.nii | | wsub-01_desc-skullstripped_T1w.nii | sub-01_space-individual_res-r1pt0_desc-preproc_T1w.nii | | msub-01_space-individual_desc-something_label-brain_mask.nii | sub-01_space-individual_label-brain_mask.nii | | c1sub-01_T1w.surf.gii | sub-01_desc-pialsurf_T1w.gii | ## Statistics At the subject level each folder contains for each run modeled: - a pair of `*_onsets.mat` / `*_onsets.tsv` The `*_onsets.mat` file contains the `names`, `onsets`, `durations`, `pmod` required by SPM to build the "multi condition" section of the model specification. The `*_onsets.tsv` is a human readable equivalent organised like BIDS `events.tsv` files. - a pair of `*_desc-confounds_regressors.mat` / `*_desc-confounds_regressors.tsv` The `*_desc-confounds_regressors.mat` file contains the `names`, `R` required by SPM to build the "multi regressor" section of the model specification. The `*_desc-confounds_regressors.tsv` is a human readable equivalent organised like BIDS derivatives `timeseries.tsv` files. ```text bidspm-stats ├── sub-01 │   └── task-taskName_space-space_FWHM-0_node-nodeName │   | │   ├── beta_0001.nii ---------- │   ├── beta_*.nii | │   ├── con_0001.nii | │   ├── con_*.nii | │   ├── mask.nii | Regular SPM output │   ├── ResMS.nii | │   ├── RPV.nii | │   ├── SPM.mat | │   ├── spmT_0001.nii | │   ├── spmT_*.nii ---------- │   | │   ├── sub-blnd01_task-taskName_space-space_desc-contrastName_label-0039_p-0pt050_k-10_MC-FWE_montage.png │   | │   ├── sub-blnd01_task-taskName_space-space_desc-afterEstimation_designmatrix.png │   ├── sub-blnd01_task-taskName_space-space_desc-beforeEstimation_designmatrix.png │   | │   ├── sub-blnd01_task-taskName_run-01_desc-confounds_regressors.mat ------ │   ├── sub-blnd01_task-taskName_run-01_desc-confounds_regressors.tsv | │   ├── sub-blnd01_task-taskName_run-01_onsets.mat | │   ├── sub-blnd01_task-taskName_run-01_onsets.tsv | Files used for model specification │   ├── sub-blnd01_task-taskName_run-*_desc-confounds_regressors.mat | │   ├── sub-blnd01_task-taskName_run-*_desc-confounds_regressors.tsv | │   ├── sub-blnd01_task-taskName_run-*_onsets.mat | │   └── sub-blnd01_task-taskName_run-*_onsets.tsv -------------------------- ... ``` ``` outputs/derivatives/bidspm-stats ├── CHANGES ├── dataset_description.json ├── derivatives │   └── bidspm-groupStats │   ├── CHANGES │   ├── dataset_description.json │   ├── jobs │   │   └── │   │   └── group │   │   ├── batch_contrasts_rfx_2023-05-06T12-49.json │   │   ├── batch_contrasts_rfx_2023_05_06T12_49.m │   │   ├── batch_group_level_model_specification_estimation_2023-05-06T12-49.json │   │   └── batch_group_level_model_specification_estimation_2023_05_06T12_49.m │   ├── LICENSE │   ├── README.md │   ├── sub-ALL_task-_space-_FWHM-6_conFWHM-0_node-dataset_contrast- │   │   ├── beta_0001.nii │   │   ├── con_0001.nii │   │   ├── mask.nii │   │   ├── ResMS.nii │   │   ├── RPV.nii │   │   ├── SPM.mat │   │   ├── spmT_0001.nii │   │   ├── task-_space-_desc-afterEstimation_designmatrix.png │   │   └── task-_space-_desc-beforeEstimation_designmatrix.png │   └── sub-ALL_task-_space-_FWHM-6_conFWHM-6_node-dataset_contrast- │   ├── beta_0001.nii │   ├── con_0001.nii │   ├── mask.nii │   ├── ResMS.nii │   ├── RPV.nii │   ├── SPM.mat │   ├── spmT_0001.nii │   ├── task-_space-_desc-afterEstimation_designmatrix.png │   └── task-_space-_desc-beforeEstimation_designmatrix.png ├── jobs │   └── │   ├── group │   │   ├── batch_smooth_con_FWHM-6_task-_2023-05-06T12-49.json │   │   └── batch_smooth_con_FWHM_6_task__2023_05_06T12_49.m │   ├── sub-292 │   │   ├── batch_contrasts_ffx_task-_space-_FWHM-6_2023-05-06T12-43.json │   │   ├── batch_contrasts_ffx_task__space__FWHM_6_2023_05_06T12_43.m │   │   ├── batch_specifyAndEstimate_ffx_task-_space-_FWHM-6_2023-05-06T12-35.json │   │   └── batch_specifyAndEstimate_ffx_task__space__FWHM_6_2023_05_06T12_35.m │   ├── sub-302 │   └── sub-307 ├── LICENSE ├── README.md ├── reports │   ├── bidspm.bib │   └── stats_model-default_es_model_citation.md ├── sub-292 │   └── task-_space-_FWHM-6 │   ├── beta_0001.nii │   ├── beta_0002.nii │   ├── ... │   ├── beta_0060.nii │   ├── con_0001.nii │   ├── con_0002.nii │   ├── con_0003.nii │   ├── con_0004.nii │   ├── con_0005.nii │   ├── con_0006.nii │   ├── mask.nii │   ├── ResMS.nii │   ├── RPV.nii │   ├── s6con_0001.nii │   ├── s6con_0002.nii │   ├── s6con_0003.nii │   ├── s6con_0004.nii │   ├── s6con_0005.nii │   ├── s6con_0006.nii │   ├── SPM.mat │   ├── spmT_0001.nii │   ├── spmT_0002.nii │   ├── spmT_0003.nii │   ├── spmT_0004.nii │   ├── spmT_0005.nii │   ├── spmT_0006.nii │   ├── sub-292_ses-_task-_run-01_desc-confounds_regressors.mat │   ├── sub-292_ses-_task-_run-01_desc-confounds_regressors.tsv │   ├── sub-292_ses-_task-_run-01_onsets.mat │   ├── sub-292_ses-_task-_run-01_onsets.tsv │   ├── sub-292_task-_space-_desc-afterEstimation_designmatrix.png │   └── sub-292_task-_space-_desc-beforeEstimation_designmatrix.png ├── sub-302 │   └── task-_space-_FWHM-6 │   ├── beta_0001.nii │   ├── beta_0002.nii │   ├── ... │   ├── beta_0154.nii │   ├── con_0001.nii │   ├── con_0002.nii │   ├── con_0003.nii │   ├── mask.nii │   ├── ResMS.nii │   ├── RPV.nii │   ├── s6con_0001.nii │   ├── s6con_0002.nii │   ├── s6con_0003.nii │   ├── SPM.mat │   ├── spmT_0001.nii │   ├── spmT_0002.nii │   ├── spmT_0003.nii │   ├── sub-302_ses-_task-_run-01_desc-confounds_regressors.mat │   ├── sub-302_ses-_task-_run-01_desc-confounds_regressors.tsv │   ├── sub-302_ses-_task-_run-01_onsets.mat │   ├── sub-302_ses-_task-_run-01_onsets.tsv │   ├── sub-302_task-_space-_desc-afterEstimation_designmatrix.png │   └── sub-302_task-_space-_desc-beforeEstimation_designmatrix.png └── sub-307 └── task-_space-_FWHM-6 ├── beta_0001.nii ├── beta_0002.nii ├── ... ├── beta_0237.nii ├── con_0001.nii ├── con_0002.nii ├── con_0003.nii ├── con_0004.nii ├── con_0005.nii ├── con_0006.nii ├── con_0007.nii ├── con_0008.nii ├── mask.nii ├── ResMS.nii ├── RPV.nii ├── s6con_0001.nii ├── s6con_0002.nii ├── s6con_0003.nii ├── s6con_0004.nii ├── s6con_0005.nii ├── s6con_0006.nii ├── s6con_0007.nii ├── s6con_0008.nii ├── SPM.mat ├── spmT_0001.nii ├── spmT_0002.nii ├── spmT_0003.nii ├── spmT_0004.nii ├── spmT_0005.nii ├── spmT_0006.nii ├── spmT_0007.nii ├── spmT_0008.nii ├── sub-307_ses-_task-_run-01_desc-confounds_regressors.mat ├── sub-307_ses-_task-_run-01_desc-confounds_regressors.tsv ├── sub-307_ses-_task-_run-01_onsets.mat ├── sub-307_ses-_task-_run-01_onsets.tsv ├── sub-307_task-_space-_desc-afterEstimation_designmatrix.png └── sub-307_task-_space-_desc-beforeEstimation_designmatrix.png ```