example-settings.txt

#===============================================================================
# Settings for freesurfer-7T-pipeline (fs-recon-7T.sh)
#===============================================================================

# Specify the path to your data
PROJECTBASEPATH="/path/to/your/data"

# file separator character (always '/' on linux/osx)
F="/"

# Specify the subjects that should be processed (separated by spaces); these
# should correspond to the naming of the folders in your $PROJECTBASEPATH
SUBJECTS="subject1 subject2 subject3"

# Specify the number of the run containing the anatomical volume (with respect to the beginning of the scanning session)
runAnatomy=5

# Specify the number of the run containing the proton-density volume (with respect to the beginning of the scanning session)
runPD=6

#===============================================================================
# Flags for processing steps
#===============================================================================
# Ask the user to check talairach transformation and skull stripping?
flag_askQuestions=true

# Do the DICOM conversion?
flag_conversion=true

# Do a rigid-body co-registration using FSL FLIRT between anatomy and pd volume?
# CAUTION: FSL needs to be installed (and in the PATH)
flag_alignPD=true

# Do the import of the divPDm.mgz file into the fs dir?
flag_reconRegister=true

# Do the recon for downsampled data (1mm)?
flag_reconDownsampled=true

# Until which step should I proceed in the downsampled (1mm) routines?
# "Step 1: motion correction and talairach transformation..."
# "Step 2: nu correction (go, get a coffee, this will take a while)..."
# "Step 3: normalization..."
# "Step 4: skull stripping..."
# "Step 5: autorecon2 and autorecon3 (go, get a coffee, this will take a while)..."
ENDSTATUS1mm=5

# Do the recon for the (normal) dataset?
flag_recon=true

# Until which step should I proceed in the (normal) routines?
# "Step 1: motion correction and talairach transformation..."
# "Step 2: nu correction (go, get a coffee, this will take a while)..."
# "Step 3: normalization..."
# "Step 4: skull stripping..."
# "Step 5: gcareg and canorm..."
# "Step 6: normalize..."
# "Step 7: maskbfs and segmentation..."
# "Step 8: Smooth and inflate for LH and RH..."
# "Step 9: smooth and autorecon3..."
ENDSTATUS=9

#===============================================================================
# Flags for the back-transformation
#===============================================================================
# Do the back-transformation into native space (flag has priority over the next two flags)?
flag_backTransform=true

# Back-transform the T1.mgz file for BrainVoyager
flag_backTransformT1=true

# Back-transform the ribbon.mgz file for BrainVoyager
flag_backTransformRibbon=true

#===============================================================================
# Computation parameters
#===============================================================================
# Number of processors to use
nProc=4

# Use GPU acceleration?
useGPU=true


#===============================================================================
# Setting for using mail notifications
#===============================================================================
# Use mail notifications?
useMail=false

# Your maildrill API key
mandrill_key="YOUR_MANDRILL_API_KEY"

# Sender email address
from_email="from@domain.tld"

# Receiver email address
to_email="to@domain.tld"

# Reply email address
reply_to="$from_email"

# "From" name
from_name="Freesurfer recon pipeline"

# Mail subject
mail_subject="Freesurfer Recon Pipeline"