poplahan.blogg.se - Tutorial surfer 9

#Tutorial surfer 9 install#
#Tutorial surfer 9 manual#

Right-click > MRI segmentation > FreeSurfer.

Select the T1 MRI (or the T1+T2 MRIs simultaneously).

Set the fiducial points manually (NAS/LPA/RPA) or compute the MNI normalization.

Optional: Import the T2 MRI for this subject, if available.

Create a new subject, set the default anatomy option to "No, use individual anatomy".

Switch to the anatomy side of the database explorer.

More instructions for setting up the environment and tuning the reconstruction here: Īlternatively, it is possible to call the FreeSurfer recon-all pipeline from Brainstorm.

#Tutorial surfer 9 manual#

We suggest instead that you load it all in Brainstorm and go back to the manual checking/editing only if it looks bad. The FreeSurfer wiki suggests that you check all the steps with FreeSurfer. Because the process may occasionally fail, always check visually the final surfaces.

Everything is ready to be imported in Brainstorm. For details see section Cortical parcellations below.ĭone. If you have an additional T2 or FLAIR image, you can improve the cortex reconstruction: Īdditional volume or surface parcellations can be computed at this stage.

Run the reconstruction (6-12 hours): recon-all -i -subjid.Set up the FreeSurfer environment in a bash environment (add these lines at the end of your $HOME/.bashrc script): export FREESURFER_HOME=/./local/freesurferĮxport SUBJECTS_DIR=/./data/ftadel/freesurferĮxport FUNCTIONALS_DIR=/./data/ftadel/freesurfer Source /./local/freesurfer/FreeSurferEnv.csh

Setenv FUNCTIONALS_DIR /./data/freesurfer/sessions Setenv SUBJECTS_DIR /./data/freesurfer/subjects setenv FREESURFER_HOME /./local/freesurfer If it says "/bin/tcsh" or "/bin/csh", this is for you. If you're not sure what csh is: type "echo $SHELL" to know what is the name of the shell that you use. Set up the FreeSurfer in a csh/tcsh environment: run the following lines, or add them at the end of your $HOME/.cshrc script for permanent change.

#Tutorial surfer 9 install#

Two options: you have a Linux system and you want to install FreeSurfer, or you don't and you want to run FreeSurfer in a Linux virtual machine. Downloading and installing FreeSurfer is easy but long (several Gb).