General S²M Output Structure

The S²M output files will be stored in the same folder as the loaded NIfTI images, within individualized folders created using the name of each loaded image (up to the first 30 characters).

All files related to a specific subject will be stored within its corresponding individualized folder.

It is highly recommended that you never manually rename files or folders. S²M attempts to skip procedures that have already been completed in order to improve processing speed. Changing the names of files or folders may break the dependency structure used by S²M and cause previously generated files to be incorrectly identified or processing steps to be repeated.

In addition to the individualized subject folders, a general folder named “0_Settings_Quality_and_Harmon_ + date/time” will also be created. This folder contains information related to the loaded cases as a group, including harmonization parameters, pre- and post-harmonization correction plots, outlier test results, and a screenshot of the S²M GUI.

Now, back to the individualized folders:

Considering a subject with a filename "sub-00001_t1wi.nii". Inside each subject's folder, you will find:

1. A text file with the subject TIV: sub-00001_t1wi_TIV.txt
2. Three folders derived from the basic CAT preprocessing: "label", "mri" and "report"
3. The results, in a folder with a name that summarizes the Modality, the Smoothing Kernel, whether a FLAIR image was used, whether harmonization was performed, and the specific date/time of this particular study (when the "Run" button was pressed). For example:

FCD Modality: FCD_Morph-SK8-Fla-Harm_2606091100

GM Modality: GM_Morph-SK8-Harm_2606091100

WM Modality: WM_Morph-SK8-Harm_2606091100

The "mri" folder will keep all NIfTI files derived from the loaded images:

1. Normalized T1WI: prefix wm
2. Deformation field: prefix y_
3. Normalized gray matter map: prefix mwp1
4. Normalized white matter map: prefix mwp2
5. Normalized CSF map: prefix mwp3
6. Native-space skull-striped, tissue normalized T1WI: prefix p0
7. Smoothed normalized gray matter map: prefix s8mwp1 (for the case of a smoothing kernel of 8 x 8 x 8 mm³)
8. Smoothed normalized white matter map: prefix s8mwp2 (for the case of a smoothing kernel of 8 x 8 x 8 mm³)
9. Smoothed normalized CSF map: prefix s8mwp3 (for the case of a smoothing kernel of 8 x 8 x 8 mm³)
10. FLAIR biased smoothed normalized gray matter map: prefix fs8mwp1 (if FCD modality with FLAIR images loaded)
11. FLAIR biased smoothed normalized white matter map: prefix fs8mwp2 (if FCD modality with FLAIR images loaded)
12. Harmonized FLAIR biased smoothed normalized gray matter map: prefix hfs8mwp1 (if FCD modality with FLAIR images loaded and harmonization procedures)
13. FLAIR biased smoothed normalized white matter map: prefix hfs8mwp2 (if FCD modality with FLAIR images loaded and harmonization procedures)

The "label" folder will generally be empty.

The "report" folder will generally contain three files: A .mat file containing a MATLAB structure with all parameters used during processing, including the resulting quality parameters for the image. The same information will also be stored in .xml and .txt files.

To modality specific output files, please visit:

• For Gray Matter Modality
• For White Matter Modality
• For Focal Cortical Dysplasia Modality