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Hello FreeSurfer Developers,
I’m attempting to run recon-all with synthstrip on v7.3.2. I get the following error each time:
reading transform from transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z error: No such file or directory error: transforms/talairach.m3z: could not open transform
I’ve tried several variations of the command below, all of which failed at the same point:
export FREESURFER_HOME=/usr/local/freesurfer/7.3.2 source $FREESURFER_HOME/SetUpFreeSurfer.sh export FS_ALLOW_DEEP=1 recon-all -all -s freesurfer -i T1.nii -sd . -synthstrip -hires -openmp 20 -parallel
It seems that -careg is being skipped for some reason. The command progresses from -canorm to -calabel which then crashes. The status file does not show careg being called at all:
status file for recon-all Fri Sep 30 16:19:18 BST 2022 #@# MotionCor Fri Sep 30 16:19:23 BST 2022 #@# Talairach Fri Sep 30 16:20:13 BST 2022 #@# Talairach Failure Detection Fri Sep 30 16:26:43 BST 2022 #@# Nu Intensity Correction Fri Sep 30 16:26:44 BST 2022 #@# Intensity Normalization Fri Sep 30 16:33:05 BST 2022 recon-all -s cluster finished without error at Fri Sep 30 16:37:38 BST 2022 #New# invocation of recon-all status file for recon-all Fri Sep 30 16:38:58 BST 2022 #@# EM Registration Fri Sep 30 16:38:58 BST 2022 #@# CA Normalize Fri Sep 30 16:42:24 BST 2022 #@# SubCort Seg Fri Sep 30 16:44:14 BST 2022 Linux chumbawumba 4.4.0-19041-Microsoft #1237-Microsoft Sat Sep 11 14:32:00 PST 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s cluster exited with ERRORS at Fri Sep 30 16:44:29 BST 2022
I have got it to run by explicitly using the -careg flag:
recon-all -all -s freesurfer -i T1.nii -sd . -synthstrip -careg -hires -openmp 24 -parallel
I also do not get this error if I omit -synthstrip.
Is there anything I’m missing here, a flag I should have specified etc.? Or is this just an unfortunate bug?
Thanks in advance! Oliver
1. FreeSurfer versions: * freesurfer-linux-ubuntu20_x86_64-7.3.2 * freesurfer-linux-centos7_x86_64-7.3.2 * freesurfer-darwin-macos-7.3.2 2. Platforms: * WSL ubuntu 20.04 * HPC centos 7 * M1 Macos Montery 12.4 3. recon-all.log: see attached