Installing Freesurfer 8.1 on CentOS8

Software Support
1

Hi,
Unlike Freesurer 8.0 that installs fine on CentOS8, 8.1 does not (errors below). I am not an administrator on the system so I cannot install CentOS7 libraries and so on. My analysis is longitudinal, so I need to run 3 times. Can anyone help with my options?

  1. Will I be affected by the symlink bug in 8.0, if I run the longitudinal pipeline? How about if I just edit surface errors?
  2. Is it a way to install 8.1 on CentOS8?
  3. If none of the above, Any idea when 8.2 will come and if it will work on CentOS8?

Thank you in advance,
Julian

kety:/usr/local/freesurfer # rpm -i freesurfer-CentOS7-8.1.0-1.x86_64.rpm
error: Failed dependencies:
bc is needed by freesurfer-8.1.0-1.x86_64
csh is needed by freesurfer-8.1.0-1.x86_64
libXp.so.6()(64bit) is needed by freesurfer-8.1.0-1.x86_64
libgomp is needed by freesurfer-8.1.0-1.x86_64
libjpeg.so.62()(64bit) is needed by freesurfer-8.1.0-1.x86_64
libnsl.so.1()(64bit) is needed by freesurfer-8.1.0-1.x86_64
libnsl.so.1(GLIBC_2.2.5)(64bit) is needed by freesurfer-8.1.0-1.x86_64
libpng12.so.0()(64bit) is needed by freesurfer-8.1.0-1.x86_64
libpng15.so.15()(64bit) is needed by freesurfer-8.1.0-1.x86_64
libpng15.so.15(PNG15_0)(64bit) is needed by freesurfer-8.1.0-1.x86_64
2

you can try installing freesurfer 8.1.0 via a container? I’ve personally tried the neurodesk fs 8.1.0 docker (Package freesurfer_8.1.0 · GitHub) and it works fine for me. Though i’m running on rocky linux 8.7.

3

Thank you for the suggestion. I am trying it. I have apptainer installed, but I struggle to get it working, it crashes after an hour I think due to a temporary or scratch directory it cannot use. Do you maybe have the command you are running? I am trying this:

apptainer exec \
      --cleanenv \
      --env SUBJECTS_DIR=/subjects \
      --env FS_SCRATCH=/scratch \
      --env TMPDIR=/scratch \
      -B ${HOST_SUBJECTS_DIR}:/subjects \
      -B ${HOST_DATA}:/data \
      -B ${HOST_SCRATCH}:/scratch \
      -B ${FS_LIC}:/opt/freesurfer/license.txt \
      ${SIF} \
      recon-all \
        -s ${FS_ID} \
        -i ${T1} \
        -3T \
        -all \
        -parallel \
        -openmp ${THREADS}
4

My HPC only has singularity 4.0.2. installed. Though i suppose singularity runs similarly to aptainer

to install:

cd $HOME
singularity build --sandbox freesurfer docker://ghcr.io/neurodesk/freesurfer_8.1.0:latest

to run recon-all

singularity run --cleanenv \
-B $HOME/freesurfer/scratch:/scratch \
$HOME/freesurfer \
recon-all -all \
-s 001 \
-i path/to/sub-001_T1w.nii.gz \
-sd path/to/SUBJECTS_DIR