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