Here is the wiki help page to setup and config your FreeSurfer:

https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Christine Farrugia
Sent: Tuesday, May 7, 2024 1:05 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] ERROR: cannot find AntsN4BiasFieldCorrectionFs in path

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Hi,

I have installed FreeSurfer (freesurfer-linux-centos7_x86_64-7.4.1) into my research group's directory on the University cluster, using the tar archive. I source it with

GROUPDIR=<path_to_group_directory>

export FREESURFER_HOME=$GROUPDIR/software/freesurfer

. $FREESURFER_HOME/SetUpFreeSurfer.sh

export PATH=$FREESURFER_HOME/bin:${PATH}

and am trying to run recon-all like so:

recon-all -s <subj_id> -i <path_to_T1_data> -T2 <path_to_T2_data> -T2pial -autorecon-all

However, FreeSurfer keeps giving the error:

ERROR: cannot find AntsN4BiasFieldCorrectionFs in path

when AntsN4BiasFieldCorrectionFs is definitely in freesurfer/bin

Any insight into the matter would be greatly appreciated 🙂

Regards,

Christine

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