search

josephdviviano / epitome

scriptit modules for fmri analysis
Other
9 stars 6 forks source link

McRetroTS error #57

Open colinhawco opened 7 years ago

colinhawco commented 7 years ago

The following line doesn't run in my script:

${McRetroTS} \ ${runfolder}/resp..phys ${runfolder}/card..phys ${tr} ${slice} ${fs} 0

Error: /scratch/colin/epitome//tmsfmri_study1_2017/P103/TMS/SESS01//RUN01//resp.04.phys: line 1: 6.6375732421875: command not found

I believe the variable ${McRetroTS} is unset, I expect its a hold over from an older version where this function was not implemented as a built in module?

josephdviviano commented 7 years ago

Why is this line running? Do you have .phys files?

josephdviviano commented 7 years ago

If so you need to configure McRetroTS as per the installation instructions.

colinhawco commented 7 years ago

yeah I have phys files, and I want to include it.

I foudn the bit in the readme I missed.

"For physiological noise regression, you must have the MATLAB compiler runtime installed, along with AFNI's McRetroTS scripts installed in /opt/MATLAB/MATLAB_Compiler_Runtime/ and /opt/mcretro/, respectively."

but to my knowledge I have no power to install anything in /opt/. The matlab module is loaded. No idea how to get mcretro into any kind of path. It doesn't appear to be a module.

josephdviviano commented 7 years ago

You can install mcretro yourself in your projects folder: https://sscc.nimh.nih.gov/sscc/dglen/McRetroTS

colinhawco commented 7 years ago

I think I already have it:

export PATH='/scratch/colin/MCR/v715/bin':$PATH export LD_LIBRARY_PATH='/scratch/colin/MCR/v715/runtime/glnxa64':$LD_LIBRARY_PAT

This worked in my previous versions of epitome.

${McRetroTS} still seems to be a non-existent variable though. It never gets set.

colinhawco commented 7 years ago

I got it to work. I had to specify the variable ${McRetroTS} as

McRetroTS=/projects/colin/applications/epitome/bin/run_McRetroTS.sh

And add an input argument, pathing to my library file as needed by the SH file. /scratch/colin/MCR/v715/

So my code now reads:

McRetroTS=/projects/colin/applications/epitome/bin/run_McRetroTS.sh

${McRetroTS} /scratch/colin/MCR/v715/ ${runfolder}/resp..phys ${runfolder}/card..phys ${tr} ${slice} ${fs} 0

I think the current version of the physio is bugged. McRetroTS seems to be included in the epitome version, but the generated code needs to be updated. The current readme doesn't seem to really cover this (the challenges of documentation, on which I am in a position to criticize exactly nobody!)

josephdviviano commented 7 years ago

Yes sorry the documentation is really out of date, and the mcretrots thing isn't used by anyone other than yourself at the minute. I should will fit (I'll leave the issue open until it is fixed).

josephdviviano commented 7 years ago

Hi Colin,

I now include all of MCR v7.15 in epitome, and have fixed init_basic to automatically set it up for you. Hopefully it works going forward without you having to mess around with the scripts!

josephdviviano commented 7 years ago

nevermind -- mcretrots takes up too much space in git LFS -- but I'm pinging the AFNI folks to make sure they host a copy of the file somehwere.

Perhaps I'll need to transition to another method for physio noise regression.

josephdviviano commented 7 years ago

Great news -- the re-wrote mcretrots in python so we don't need to bother with this MCR thing any longer.

josephdviviano commented 7 years ago

I'll update the module to use RetroTS.py