I’m trying to view multiple neuroimaging datatypes (.nii) on a remote cluster using the gui viewer Freeview (part of freesurfer).
I’m only noticing slowness and significant lag in Freeview when I’m trying to open multiple 4D images (in this case, bold fMRI scans). I have tried to allocate more cores and memory to my interactive session but this hasn’t improved performance. Is there something else I can try?
FreeSurfer utilizes OpenMP for parallelization in Freeview. You therefore need to be sure to set the environment variable $OMP_NUM_THREADS to instruct Freeview on the available resources.
On SGE systems, the variable $NSLOTS stores the number of processing slots allocated to your job which you can use to set with:
export OMP_NUM_THREADS=$NSLOTS
On SLURM systems, the variable $SLURM_CPUS_PER_TASK stores the number of processing slots allocated to your job which you can use to set with:
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
Could you provide context to this? for example what is Freeview or FreeSurfer? Providing a link too would be great.
Absolutely!
FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. This is a very popular software and is routinely used in brain MRI research. Here is link to the official FreeSurfer wiki.
Freeview is the visualization plugin for FreeSurfer. Similar to the FSLeyes plugin for FSL or the standalone visualization software MRIcroGL, these softwares are used to view medical imaging. These are all extremely popular visualization tools within the neuroimaging and neuro-research community. Here is a link to the official Freeview guide.