Question about `-m` option

[jacobtfisher]

Hi there. Thanks for putting together such a useful tool. I just have a quick question about the -m flag. The description provided says:

   Optional arguments:
    -m : Execution mode:
         Input can either be 's' (for serial execution on a
         single machine)[default], 'c' (for execution on a
         computing cluster) or a path to a file (for execution
         on a computing cluster, subject to the specifications
         defined in the file).

I'd like to be able to use this flag rather than breaking up the cohort file, since (I assume) it would let me run xcpEngine in parallel while still generating the group level outputs (which don't seem to work when the cohort file is split into individual subjects for running in parallel). What sort of file would I specify in order to use the -m flag? Is this option compatible with SLURM?

Thank you!

[a3sha2]

Hi @jacobtfisher it is difficult to use -m with singularity or docker images but there is a trick here https://xcpengine.readthedocs.io/containers/index.html#using-slurm-to-parallelize-across-subjects ?

[jacobtfisher]

Hi @a3sha2 -- thanks for getting back to me! I'm looking at the page now and I'm not seeing anything about the -m option. Maybe I'm looking in the wrong place. Splitting up the cohort files to run in parallel is what I'm doing right now, but that option doesn't create the groupwise analyses (unless I'm doing something incorrectly). I'd like to be able to see the qcfc output for all subjects but run the job in parallel.

Thanks again!

[a3sha2]

I get you @jacobtfisher. You cant sue -m flag with singularity or docker image. You can still run qcfc after you completion of xpcengine for all the subjects . We add utility command that does that. https://xcpengine.readthedocs.io/utils/qcfc.html#qcfc

if you are using docker image:

  --entrypoint /xcpEngine/utils/qcfc.R \
  pennbbl/xcpEngine:latest \
  –c <cohort> \
  -o <output root> \
  [-s <multiple comparisons correction> \
   -t <significance threshold> \
   -n <confound> \
   -y <conformula>]

if you are suing singularity image, it is the same way

singularity exec  xcpengine.simg   /xcpEngine/utils/qcfc.R \
  –c <cohort> \
  -o <output root> \
  [-s <multiple comparisons correction> \
   -t <significance threshold> \
   -n <confound> \
   -y <conformula>]