How long does recon all take FreeSurfer?
How long does it take for recon-all to finish processing one subject? 20-24 hours.
How do I open a FreeSurfer file?
To load a surface, click File -> Load Surface , and select an image in the surf directory, such as lh.
What is recon all?
Overview: Reconstructing the Cortical Surface Later on, you will learn how to execute multiple recon-all commands simultaneously, which will save you a considerable amount of time. Recon-all stands for reconstruction, as in reconstructing a two-dimensional cortical surface from a three-dimensional volume.
What is Fsaverage FreeSurfer?
During installation, FreeSurfer copies a subject called ‘fsaverage’ to $FREESURFER_HOME/subjects/fsaverage . fsaverage is a template brain based on a combination of 40 MRI scans of real brains. The fsaverage subject folder contains all the files that a normal subject reconstruction would yield.
Is FreeSurfer open source?
FreeSurfer is an open source package for the analysis and visualization of structural, functional, and diffusion neuroimaging data from cross-sectional and longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging.
What is recon-all in FreeSurfer?
recon-all : Performs all, or any part of, the FreeSurfer cortical reconstruction process. Note: arguments are described in greater detail in the Description section (further below). single DICOM file from the T1 MRI series. If you have more than one T1, then use: -i file1.dcm -i file2.dcm single NIFTI file from series
How do I import subject data from FreeSurfer?
Source the correct version of FreeSurfer: Import your data and create a subject data directory. This is done once using the following command: recon-all -i invol1 -i invol2 -subjid your_subject_name where invol1 and invol2 are paths to your input files.
Why are my fsaverage files being deleted when upgrading FreeSurfer?
If a previous version of fsaverage is detected which does not include these new files, then recon-all will delete the old fsaverage and create a new symlink. As a result, any files manually created by the user inside the fsaverage directory are potentially at risk of being deleted when upgrading Freesurfer versions.
Should autorecon3 be re-ran to compute statistics for new surfaces?
Note that autorecon3 should also be re-ran to compute statistics based on the new surfaces. For example: To manually edit segmenation, run the following command (make sure that your SUBJECTS_DIR environment variable is properly set).