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OUTPUT_FILES.md

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Output files

Segmentation module

The segmentation module outputs the files shown in the table below. The two primary output files are the aparc.DKTatlas+aseg.deep.mgz file, which contains the FastSurfer segmentation of cortical and subcortical structures based on the DKT atlas, and the aseg+DKT.stats file, which contains summary statistics for these structures. Note, that the surface model (downstream) corrects these segmentations along the cortex with the created surfaces. So if the surface model is used, it is recommended to use the updated segmentations and stats (see below).

directory filename module description
mri aparc.DKTatlas+aseg.deep.mgz asegdkt cortical and subcortical segmentation
mri aseg.auto_noCCseg.mgz asegdkt simplified subcortical segmentation without corpus callosum labels
mri mask.mgz asegdkt brainmask
mri orig.mgz asegdkt conformed image
mri orig_nu.mgz asegdkt biasfield-corrected image
mri/orig 001.mgz asegdkt original image
scripts deep-seg.log asegdkt logfile
stats aseg+DKT.stats asegdkt table of cortical and subcortical segmentation statistics

Cerebnet module

The cerebellum module outputs the files in the table shown below. Unless switched off by the --no_cereb argument, this module is automatically run whenever the segmentation module is run. It adds two files, an image with the sub-segmentation of the cerebellum and a text file with summary statistics.

directory filename module description
mri cerebellum.CerebNet.nii.gz cerebnet cerebellum sub-segmentation
stats cerebellum.CerebNet.stats cerebnet table of cerebellum segmentation statistics

HypVINN module

The hypothalamus module outputs the files in the table shown below. Unless switched off by the --no_hypothal argument, this module is automatically run whenever the segmentation module is run. It adds three files, an image with the sub-segmentation of the hypothalamus and a text file with summary statistics.

directory filename module description
mri hypothalamus.HypVINN.nii.gz hypvinn hypothalamus sub-segmentation
mri hypothalamus_mask.HypVINN.nii.gz hypvinn hypothalamus sub-segmentation mask
stats hypothalamus.HypVINN.stats hypvinn table of hypothalamus segmentation statistics

If a T2 image is also passed, the following images are created.

directory filename module description
mri T2_nu.mgz hypvinn biasfield-corrected T2 image
mri T2_nu_reg.mgz hypvinn co-registered T2 to orig image

Surface module

The surface module is run unless switched off by the --seg_only argument. It outputs a large number of files, which generally correspond to the FreeSurfer nomenclature and definition. A selection of important output files is shown in the table below, for the other files, we refer to the FreeSurfer documentation. In general, the "mri" directory contains images, including segmentations, the "surf" folder contains surface files (geometries and vertex-wise overlay data), the "label" folder contains cortical parcellation labels, and the "stats" folder contains tabular summary statistics. Many files are available for the left ("lh") and right ("rh") hemisphere of the brain. Symbolic links are created to map FastSurfer files to their FreeSurfer equivalents, which may need to be present for further processing (e.g., with FreeSurfer downstream modules).

After running this module, some of the initial segmentations and corresponding volume estimates are fine-tuned (e.g., surface-based partial volume correction, addition of corpus callosum labels). Specifically, this concerns the aseg.mgz , aparc.DKTatlas+aseg.mapped.mgz, aparc.DKTatlas+aseg.deep.withCC.mgz, which were originally created by the segmentation module or have earlier versions resulting from that module.

The primary output files are pial, white, and inflated surface files, the thickness overlay files, and the cortical parcellation (annotation) files. The preferred way of assessing this output is the FreeView software. Summary statistics for volume and thickness estimates per anatomical structure are reported in the stats files, in particular the aseg.stats, and the left and right aparc.DKTatlas.mapped.stats files.

directory filename module description
mri aparc.DKTatlas+aseg.deep.withCC.mgz surface cortical and subcortical segmentation incl. corpus callosum after running the surface module
mri aparc.DKTatlas+aseg.mapped.mgz surface cortical and subcortical segmentation after running the surface module
mri aparc.DKTatlas+aseg.mgz surface symlink to aparc.DKTatlas+aseg.mapped.mgz
mri aparc+aseg.mgz surface symlink to aparc.DKTatlas+aseg.mapped.mgz
mri aseg.mgz surface subcortical segmentation after running the surface module
mri wmparc.DKTatlas.mapped.mgz surface white matter parcellation
mri wmparc.mgz surface symlink to wmparc.DKTatlas.mapped.mgz
surf lh.area, rh.area surface surface area overlay file
surf lh.curv, rh.curv surface curvature overlay file
surf lh.inflated, rh.inflated surface inflated cortical surface
surf lh.pial, rh.pial surface pial surface
surf lh.thickness, rh.thickness surface cortical thickness overlay file
surf lh.volume, rh.volume surface gray matter volume overlay file
surf lh.white, rh.white surface white matter surface
label lh.aparc.DKTatlas.annot, rh.aparc.DKTatlas.annot surface symlink to lh.aparc.DKTatlas.mapped.annot
label lh.aparc.DKTatlas.mapped.annot, rh.aparc.DKTatlas.mapped.annot surface annotation file for cortical parcellations, mapped from ASEGDKT segmentation to the surface
stats aseg.stats surface table of cortical and subcortical segmentation statistics after running the surface module
stats lh.aparc.DKTatlas.mapped.stats, rh.aparc.DKTatlas.mapped.stats surface table of cortical parcellation statistics, mapped from ASEGDKT segmentation to the surface
stats lh.curv.stats, rh.curv.stats surface table of curvature statistics
stats wmparc.DKTatlas.mapped.stats surface table of white matter segmentation statistics
scripts recon-all.log surface logfile