Re: [Freesurfer] ERROR: cannot find AntsN4BiasFieldCorrectionFs in path

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

External Email - Use Caution 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 The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.