Hi,
I’m performing Freesurfer’s recon-all
prior to running fmriprep, using the following:
output_dir=$bids_root_dir/derivatives/freesurfer
#need /bin/perl in order to run the nu_correct portion of recon-all
export SUBJECTS_DIR=$output_dir
export FS_LICENSE=${FREESURFER_HOME}/license.txt
export MINC_BIN_DIR=${FREESURFER_HOME}/mni/bin
export MINC_LIB_DIR=${FREESURFER_HOME}/mni/lib
export MY_PERL=$(which perl)
if [ ! -d $output_dir/sub-${s} ]; then
#Run recon-all
if [ -f $bids_root_dir/sub-${s}/anat/sub-${s}*_T2w.nii.gz ]; then
#Include T2w anatomical image in recon-all processing stream
recon-all \
-s sub-{$s} \
-i $bids_root_dir/sub-${s}/anat/sub-${s}_T1w.nii.gz \
-T2 $bids_root_dir/sub-${s}/anat/sub-${s}_T2w.nii.gz \
-T2pial \
-all \
-openmp 4
else
#No T2w anatomical image in recon-all processing stream
recon-all \
-s sub-{$s} \
-i $bids_root_dir/sub-${s}/anat/sub-${s}_T1w.nii.gz \
-all \
-openmp 4
fi
fi
In reading the documentation for surface reconstruction though, I see that there are additional reconstruction steps, inclusion of ANTs brain masks, etc, so I was wondering if running Freesurfer beforehand using my method will produce comparable results compared to fmriprep’s built in method for running Freesurfer?
Thanks