.. _output_files: Output Files ============= Here, we will describe the output files of many SimNIBS see :ref:`file_formats` for a detailed description of each file type Head Segmentation ------------------ :ref:`charm_docs` generates a folder :file:`m2m_/` with the segmentation results and the head mesh :file:`.msh` for the FEM simulations. Simulations ------------- The final simulation results are in the *Output Folder*, which can be set in the GUI or in scripts. By default, this folder is called :file:`simnibs_simulation/`, and is located in the same folder as the mesh file. Below, we have: * :file:`sub_id`: Subject ID (eg. ernie) * :file:`poslist_nr`: Number of simulation in :ref:`poslist ` * :file:`cond_type`: :ref:`Type of conductivity used ` * :file:`position_nr`: :ref:`Coil position number `. * :file:`coil_name`: Name of TMS coil model. TDCS '''' * :file:`_TDCS__.msh` *Gmsh* mesh file with tDCS simulation results * :file:`_TDCS__el_currents.geo` *Gmsh* *.geo* file with simplified tDCS electrode models for visualization TMS ''' * :file:`_TMS_-__.msh` *Gmsh* mesh file with TMS simulation results * :file:`_TMS_-__coil_pos.geo` *Gmsh* *.geo* file with a simplified coil model showing it’s center and axes. For *.ccd* coil models, this is a more detail model showing dipoles. Others ''''''' * :file:`simnibs_simulation_yyyymmdd.log` Simulation log * :file:`simnibs_simulation_yyyymmdd.mat` Simulation configuration file, can be used to re-run the simulation * :file:`fields_summary.txt` A few summary quantities for each field Post-Processing '''''''''''''''' In the section below, we will use * For tDCS simulations: :file:`=TDCS__` * For TMS simulations: :file:`=TMS_-__` Surface Mapping ~~~~~~~~~~~~~~~~ * :file:`subject_overlays/` Surface overlays with fields in the subject specific space. Generated if the **Interpolate to cortical surface** (GUI) or the **map_to_surf** (script) are set * :file:`fsavg_overlays/` Surface overlays with fields in FsAverage space. Generated if the **Interpolate to FsAverage surface** (GUI) or the **map_to_fsavg** (script) are set Inside the folders, we have * :file:`__.msh` Transformed result as a Gmsh *.msh* file for easy visualization * :file:`_...` FreeSurfer generic overlay with given quantity (such as **magn** or **normal**) related to a given field. Volume Mapping ~~~~~~~~~~~~~~ * :file:`subject_volumes/` NIfTI volumes with fields in a subject specific space. Generated if **Interpolate to a nifiti volume** (GUI) or **map_to_vol** (scripts) are set. * :file:`mni_volumes/` NIfTI volumes with fields in MNI space. Generated if **Transform to MNI space** (GUI) or **map_to_mni** (scripts) are set. Inside the folders, we have *NIfTI* files with the field values. For vector fields such as **E** and **J**, the *NIfTI* files are composed of 3 volumes, each corresponding to a direction