Outputs of bidspm
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…).
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 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.
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
│ │ └── <taskLabel>
│ │ └── 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-<taskLabel>_space-<spaceLabel>_FWHM-6_conFWHM-0_node-dataset_contrast-<taskLabel>
│ │ ├── beta_0001.nii
│ │ ├── con_0001.nii
│ │ ├── mask.nii
│ │ ├── ResMS.nii
│ │ ├── RPV.nii
│ │ ├── SPM.mat
│ │ ├── spmT_0001.nii
│ │ ├── task-<taskLabel>_space-<spaceLabel>_desc-afterEstimation_designmatrix.png
│ │ └── task-<taskLabel>_space-<spaceLabel>_desc-beforeEstimation_designmatrix.png
│ └── sub-ALL_task-<taskLabel>_space-<spaceLabel>_FWHM-6_conFWHM-6_node-dataset_contrast-<taskLabel>
│ ├── beta_0001.nii
│ ├── con_0001.nii
│ ├── mask.nii
│ ├── ResMS.nii
│ ├── RPV.nii
│ ├── SPM.mat
│ ├── spmT_0001.nii
│ ├── task-<taskLabel>_space-<spaceLabel>_desc-afterEstimation_designmatrix.png
│ └── task-<taskLabel>_space-<spaceLabel>_desc-beforeEstimation_designmatrix.png
├── jobs
│ └── <taskLabel>
│ ├── group
│ │ ├── batch_smooth_con_FWHM-6_task-<taskLabel>_2023-05-06T12-49.json
│ │ └── batch_smooth_con_FWHM_6_task_<taskLabel>_2023_05_06T12_49.m
│ ├── sub-292
│ │ ├── batch_contrasts_ffx_task-<taskLabel>_space-<spaceLabel>_FWHM-6_2023-05-06T12-43.json
│ │ ├── batch_contrasts_ffx_task_<taskLabel>_space_<spaceLabel>_FWHM_6_2023_05_06T12_43.m
│ │ ├── batch_specifyAndEstimate_ffx_task-<taskLabel>_space-<spaceLabel>_FWHM-6_2023-05-06T12-35.json
│ │ └── batch_specifyAndEstimate_ffx_task_<taskLabel>_space_<spaceLabel>_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-<taskLabel>_space-<spaceLabel>_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-<sesLabel>_task-<taskLabel>_run-01_desc-confounds_regressors.mat
│ ├── sub-292_ses-<sesLabel>_task-<taskLabel>_run-01_desc-confounds_regressors.tsv
│ ├── sub-292_ses-<sesLabel>_task-<taskLabel>_run-01_onsets.mat
│ ├── sub-292_ses-<sesLabel>_task-<taskLabel>_run-01_onsets.tsv
│ ├── sub-292_task-<taskLabel>_space-<spaceLabel>_desc-afterEstimation_designmatrix.png
│ └── sub-292_task-<taskLabel>_space-<spaceLabel>_desc-beforeEstimation_designmatrix.png
├── sub-302
│ └── task-<taskLabel>_space-<spaceLabel>_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-<sesLabel>_task-<taskLabel>_run-01_desc-confounds_regressors.mat
│ ├── sub-302_ses-<sesLabel>_task-<taskLabel>_run-01_desc-confounds_regressors.tsv
│ ├── sub-302_ses-<sesLabel>_task-<taskLabel>_run-01_onsets.mat
│ ├── sub-302_ses-<sesLabel>_task-<taskLabel>_run-01_onsets.tsv
│ ├── sub-302_task-<taskLabel>_space-<spaceLabel>_desc-afterEstimation_designmatrix.png
│ └── sub-302_task-<taskLabel>_space-<spaceLabel>_desc-beforeEstimation_designmatrix.png
└── sub-307
└── task-<taskLabel>_space-<spaceLabel>_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-<sesLabel>_task-<taskLabel>_run-01_desc-confounds_regressors.mat
├── sub-307_ses-<sesLabel>_task-<taskLabel>_run-01_desc-confounds_regressors.tsv
├── sub-307_ses-<sesLabel>_task-<taskLabel>_run-01_onsets.mat
├── sub-307_ses-<sesLabel>_task-<taskLabel>_run-01_onsets.tsv
├── sub-307_task-<taskLabel>_space-<spaceLabel>_desc-afterEstimation_designmatrix.png
└── sub-307_task-<taskLabel>_space-<spaceLabel>_desc-beforeEstimation_designmatrix.png