Gear that runs FreeSurfer v7.2.0 Release (July 19, 2021) based on the official FS docker container.
To run this gear you need to select structural MRI file(s) as inputs and set configuration parameters. Minimally, the "anatomical" input file and a Freesurfer license need to be provided.
Anatomical NIfTI file, DICOM archive, or previous freesurfer-recon-all zip archive (required for gear-postprocessing-only option).
A user-created file containing special options to include in the command string. The file should contain as the first item the name of the command, and the items following it on rest of the line will be passed as the extra options. See Freesurfer documentation for more information and examples.
A license is required for this gear to run but it does not have to be provided as an input file. There are three ways to provide the license to this gear. Obtaining a license is free. If you select a file here, it will be copied into the $FSHOME directory when the gear runs before launching recon-all.
Additional anatomical NIfTI files. These will be averaged together to provide for better motion correction.
T2 or FLAIR data to improve pial surfaces. This can be NIfTI or DICOM. The -T2pial or -FLAIRpial flags will need to be added in the reconall_options configuration parameter (see below).
Note: arguments that start with "gear-" are not passed to recon-all. They control pre- or post-processing operations.
Generate an automated segmentation of four different brainstem structures from the input T1 scan: medulla oblongata, pons, midbrain and superior cerebellar peduncle (SCP). See: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures for more info. Choosing this option will write <subject_id>_brainstemSsVolumes.v2.csv to the final results. The values in that spreadsheet will also be attached to the analysis as "Custom Information" ("info" metadata) so they can be found using search and in views. (Default=true)
Convert FreeSurfer stats files to CSV. (Default=true). Converts a subcortical stats file created by recon-all and/or mri_segstats (e.g., aseg.stats) into a table in which each line is a subject and each column is a segmentation. The values are the volume of the segmentation in mm3 or the mean intensity over the structure. Also Converts all cortical stats file created by recon-all and or mris_anatomical_stats (e.g., ?h.aparc.stats) into a table in which each line is a subject and each column is a parcellation. By default, the values are the area of the parcellation in mm2. These tables will be written to .csv files that will be available in the final results. The values in the tables will also be attached to the analysis as "Custom Information" ("info" metadata) so they can be found using search and in views. (Default=true)
Convert selected surfaces in subject/surf to obj in output. This allows the surfaces to be readily viewed on the Flywheel platform. (Default = true)
Convert selected FreeSurfer volume files (mgz) to NIfTI format. This allows the volumes to be readily viewed on the Flywheel platform. (Default=true)
Do everything except actually execute recon-all. This is useful for debugging. (Default = false)
Text from license file generated during FreeSurfer registration. Copy the contents of the license file and paste it into this argument. There are three ways to provide the license to this gear.
After running recon-all run Segmentation of hypothalamic subunits (mri_segment_hypothalamic_subunits) on the subject. See: https://surfer.nmr.mgh.harvard.edu/fswiki/HypothalamicSubunits For more information.
Generates an automated segmentation of the hippocampal subfields based on a statistical atlas built primarily upon ultra-high resolution (~0.1 mm isotropic) ex vivo MRI data. See: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala for more info. Choosing this option will write <subject_id>_HippocampalSubfields.csv to the final results. The values in this spreadsheet will also be attached to the analysis as "Custom Information" ("info" metadata) so they can be found using search and in views. (Default=true)
Produce a parcellation of the thalamus into 25 different nuclei, using a probabilistic atlas built with histological data. Choosing this option will produce 3 files in the subject's mri directory: ThalamicNuclei.v12.T1.volumes.txt, ThalamicNuclei.v12.T1.mgz, and ThalamicNuclei.v12.T1.FSvoxelSpace.mgz, and 2 files in the stats directory: thalamic-nuclei.lh.v12.T1.stats and thalamic-nuclei.rh.v12.T1.stats. See: https://surfer.nmr.mgh.harvard.edu/fswiki/ThalamicNuclei for more info. (Default=false)
Gear Log verbosity level (INFO|DEBUG)
Runs the xhemireg and surfreg scripts on your subject after having run recon-all in order to register the subject's left and inverted-right hemispheres to the fsaverage_sym subject. The fsaverage_sym subject is a version of the fsaverage subject with a single the left-right symmetric pseudo-hemisphere. (Default=true).
Number of CPUs/cores use. The default is to use all available cores.
Command line option to run recon-all in parallel. By default, it instructs the binaries to use 4 processors (cores), meaning, 4 threads will run in parallel in some operations. Adjust n_cpus for more (or less) than 4 cores. NOTE: this option causes the gear to fail stochastically so recon-all is automatically retried if it fails the first time. One of the final lines of the log will say what happened. (Default=True)
Command line options to the recon-all algorithm. By default we enable '-all' and '-qcache'. '-all' runs the entire pipeline and '-qcache' will resample data onto the average subject (called fsaverage) and smooth it at various FWHM (full-width/half-max) values, usually 0, 5, 10, 15, 20, and 25mm, which can speed later processing. Note that modification of these options will result in failure if the options are not recognized. (Default='-all -qcache')
After running recon-all, run gtmseg on the subject. This creates a high-resolution segmentation gtmseg.mgz. This should take about an hour or two. gtmseg.mgz will use aseg.mgz for subcortical structures, ?h.aparc.annot for cortical structures, and will estimate some extra-cerebral structures. (Default=False).
Desired subject ID. This is used to name the resulting FreeSurfer output directory. The subject_id can only have file-name-safe characters (no spaces, special characters, etc.) because this will be used as the name of a directory for the subject. NOTE: If using a previous Gear output as input the subject code will be parsed from the input archive.
Allows post-processing steps (such as gear-hypothalamic_subunits, gear-brainstem_structures, etc) to be run WITHOUT rerunning recon-all. For this option to work, a completed recon-all output zip file must be passed as input to this gear.
This gear runs recon-all on the provided inputs with the given configuration options. See https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki in general and https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable in particular for complete details.
All files that are the results of recon-all in the Freesurfer subject directory are compressed into a single zip archive called "freesurfer-recon-all_subjectID_analysisID.zip", e.g. "freesurfer-recon-all_subj001_62e98f6939a660fff35225ff.zip". See the "Introduction to Freesurfer Output" tutorial here for details.
This gear was created using the bdis-app-template. For documentation on how to run the tests in this gear, please see that README file.