Jon Cluce

> After appending the path, now running into the following issue in the singularity image when running recon-all: > > ``` > Standard error: > Can't locate MNI/Startup.pm in @INC...

After a bit more digging, for me the surprising environment variables (e.g., the ones starting with `/usr/local/freesurfer`) were [coming from my host environment](https://sylabs.io/guides/3.7/user-guide/environment_and_metadata.html#environment-from-the-host). Starting a container with `--cleanenv` (`singularity run...

Not sure if this helps with > But from what I remember, I had to manually append a few things to my container PATH for freesurfer and miniconda, for Example:...

As noted > [T]here is an issue with the number of threads being estimated by the callback, or the gantt chart creation script is pulling in the wrong numbers. Some...

My only hesitance is the potentially misleading `runtime_threads` ― maybe that should be fixed before restoring this functionality?

> Was this fixed? What needs doing? I haven't fixed it (yet at least). The issue is that the chart uses `runtime_threads` from the callback log as a count of...

An existing unit test does https://github.com/nipy/nipype/blob/6c060304f380c46b2f05c5afdc7171dbbdfadc58/nipype/interfaces/base/tests/test_resource_monitor.py#L76-L78 which is similar to [what we're doing for now in C-PAC](https://github.com/FCP-INDI/C-PAC/blob/e63d16c61c217a5df8a8ef620af32e315e7369f5/CPAC/utils/monitoring/monitoring.py#L63-L64): ```Python if runtime_threads != 'N/A': runtime_threads = math.ceil(runtime_threads/100) ``` My concern is that,...

I ran into this issue as well and [fixed it](https://github.com/nipy/nipype/tree/a08ee57aa54868a6ce85f0799dfe4fd7cc00df3e) for [my own purpose](https://github.com/FCP-INDI/C-PAC/issues/1404#issuecomment-756383588). I'll put in a PR with the fix.

With the changes in #3290, ```Python from nipype.utils.draw_gantt_chart import generate_gantt_chart generate_gantt_chart('profiler.log', cores=4) ``` with [`profiler.log`](https://gist.github.com/SiegfriedWagner/891bb05bff3cb8224f23915634672a83) from [this issue](https://github.com/nipy/nipype/issues/2982#issue-475717026) results in a chart like this: [](https://github.com/nipy/nipype/files/5789337/profiler.log.html.zip) In the PR's comments, [the...

#### "No module named 'nipy'" > I have built a docker image for which I would like to install this library. I am able to install nipy (`RUN pip install...