Mac compatibility: Avoid PCRE grep in recon-surf, stat formatting and mapfile

[dkuegler]

Avoid using grep -P, instead use grep -E and some bash instructions.

This PR addresses #668 and was introduced by #652.

Needs testing to see if grep 2.6 / mac versions of grep on mac support the extended grep syntax.

This PR also addresses 2 more Mac compatibility issues:

• The use of mapfile in run_fastsurfer and brun_fastsurfer (the latter will just not be compatible for some specific flags/arguments)
• the use of stat which uses -c on Linux (GNU coreutils version) and -f for similar things on macOS (BSD version)

[m-reuter]

This works on my Mac. I am getting a print out
A min-conformedconformed image ... which looks weird.

Also I wonder if we should use this PR to fix the other Mac issues:

• the BSD tool stat in Mac does not have the -c flag (I think it uses -f flag for format)
• the missing mapfile

[dkuegler]

This works on my Mac. I am getting a print out A min-conformedconformed image ... which looks weird.

Also I wonder if we should use this PR to fix the other Mac issues:

* the BSD tool `stat` in Mac does not have the -c flag (I think it uses -f flag for format)

* the missing `mapfile`

Let's use this issue for that. The grep issue I was fixing here is a mac-only issue.

I will fix the mapfile thing very quickly (this is just an information things, so no damage, just going to skip that for old bash versions).
I will see about stat as well

[dkuegler]

Still working on stat
mapfile changes are untested on macos

[m-reuter]

I tested mapfile changes and it works (also tested --threads 4 for parallel).

One other thing, I get the run time only in full hours : #@#%# recon-surf-run-time-hours 0.000

Probably due to first output line: time command failing, not using time...
while a time command is available on Mac, probably uses a different format.
Update: I just saw that on Linux it also only reports the full hours. So we should probably report also minutes in both cases and we should check if the time command failing printout should be changed to a message that looks less like an error or warning, maybe "unexpected time command (maybe on MAC), using ??? instead"

[m-reuter]

I still get ./FastSurfer/run_fastsurfer.sh: line 828: mapfile: command not found. Running a test now.

[dkuegler]

I still get ./FastSurfer/run_fastsurfer.sh: line 828: mapfile: command not found. Running a test now.

What do you get, if you run bash --version ?

[m-reuter]

inside the scripts it uses the system bash, which is this:

> /bin/bash --version
GNU bash, version 3.2.57(1)-release (arm64-apple-darwin24)
Copyright (C) 2007 Free Software Foundation, Inc.

in my terminal I have a newer one (5.something) via home-brew, but system bash is still old, and that is the one that gets used via the bash shebang.

[dkuegler]

So the difference is that when we call bash --version, it is different to ./reconsurf.sh which uses the other bash .... This is so confusing.

[m-reuter]

it can be different depending on what other bash is installed on the system and in the path. On normal systems, it should be the same.