NITRC mri_reface Forum: help

RE: Basic setup and usage for native Mac and Linux

Christopher Schwarz — Thu, 04 Jun 2026 23:52:56 GMT

Kazim,
I'm sorry, I have limited ability to help you here. I've never tried to do this in Windows or ever used WSL. run_mri_reface_docker.sh is bash code, so you can view and/or modify the source if some changes are needed for your WSL environment. 
 In this line,  File not found: C:/Users/kjafri/AppData/Local/Temp/tmp.hiSWIStylc/inputs/input we are seeing a windows-style path: ("C:/") rather than a Linux-style path ("/c/"). The error is coming from inside the Docker, so we shouldn't be seeing a path like that. My best guess is that mktemp -d (line 56 of run_mri_reface_docker.sh) is not behaving appropriately for the WSL/MINGW/Linux-emulating environment. This probably means that you have an environment value $TMPDIR that contains something like "C:/" when inside WSL you want something like "/c/" (or nothing at all, and let it be the default). You appear to be using some sort of AI-based translation layer ("Gordon"), and it may be the culpret of making changes to your environment (TMPDIR) that aren't appropriate here. 
 Chris

RE: Basic setup and usage for native Mac and Linux

Kazim Jafri — Thu, 04 Jun 2026 17:57:31 GMT

I gave up on the manual compiling setup as I kept facing issues regarding implementation (not being able to find entities, etc.). So, I tried setting up the docker environment on Windows by leveraging WSL. There was no problem with setting up the image, but when I attempt to run the .sh, I get the following errors.
PHILADELPHIA+kjafri@RST-LTKJAFRI MINGW64 ~/Downloads/mri_reface_docker $ bash run_mri_reface_docker.sh /c/Users/kjafri/Downloads/mri_reface_docker/input /c/Users/kjafri/Downloads/mri_reface_docker/output Error using ADIR_ReFace File not found: C:/Users/kjafri/AppData/Local/Temp/tmp.hiSWIStylc/inputs/input
What's next:     Debug this container error with Gordon → docker ai "help me fix this container error" cp: cannot stat '/tmp/tmp.hiSWIStylc/outputs/*': No such file or directory
I'm wondering if you can provide some insights as to where I may be going wrong.

RE: Basic setup and usage for native Mac and Linux

Christopher Schwarz — Wed, 03 Jun 2026 16:37:31 GMT

It's not something I remember encountering in the one time (so far) that I built this on Apple. When I Google your error, it suggests that disabling SSE would probably remove the Intel-specific flag. The niftyreg functionality mri_reface is using doesn't require any of the optional features, so for any niftyreg build problems I would disable whatever you can via cmake (here, SSE, but if errors with libjpeg, disable jpeg, etc.) and try again. The "ccmake" GUI interface to cmake would help you see what options are available. 
Chris

RE: Basic setup and usage for native Mac and Linux

Kazim Jafri — Wed, 03 Jun 2026 15:41:41 GMT

Hi Chris,

I running across some errors and I was hoping you could help.

I cloned both repos (ANTS and Niftyreg) into our home directory, created the build folders, but ran into an error for niftyreg:

corelabadmin@Corelab-Mac-Studio01-PRD build % make
[ 1%] Building CXX object reg-lib/CMakeFiles/_reg_maths.dir/cpu/Maths.cpp.o
clang++: error: unsupported option '-msse3' for target 'arm64-apple-darwin25.5.0'
make[2]: *** [reg-lib/CMakeFiles/_reg_maths.dir/cpu/Maths.cpp.o] Error 1
make[1]: *** [reg-lib/CMakeFiles/_reg_maths.dir/all] Error 2
make: *** [all] Error 2
corelabadmin@Corelab-Mac-Studio01-PRD build % cd ..
corelabadmin@Corelab-Mac-Studio01-PRD niftyreg % cd ..

I suspect that it is anticipating x86 architecture instead of the more recent ARM architecture on Mac computers.

Any help that can be provided would be appreciated.

RE: PET refacing

Christopher Schwarz — Tue, 02 Jun 2026 16:50:05 GMT

Paul, At this time, FBB and FBP are doing the same thing behind the scenes. PIB and NAV use one template based on PIB, and the other F18 tracers use another template based on FBP. It's possible that some future version may need to differentiate them, but currently that pair are treated the same internally.
 Chris

PET refacing

Paul Wright — Tue, 02 Jun 2026 14:50:00 GMT

Hi
 
Just wondering what the difference is between the "FBP" and "FBB" image types. We have both Florbetapir and Florbetaben scans. Both options for `mri_reface ... -imType` are logged as "Target image type: Amyloid PET (F18)". Do they use the same atlas behind the scenes?
 
Thanks
Paul

RE: Basic setup and usage for native Mac and Linux

Jesse Mahan — Fri, 29 May 2026 13:30:23 GMT

Thanks. Really appreciate the information. We'll try to implement on the Mac first. If we don't have success, then we'll try with Docker.

RE: Basic setup and usage for native Mac and Linux

Christopher Schwarz — Wed, 27 May 2026 15:29:12 GMT

Jesse,
Firstly, if you're not pretty comfortable in Linux to compile and set up all the dependencies, I would recommend skipping the Mac step and running on Linux using the Docker image. Docker relieves you of having to do any of that, but the Docker image is x86/x64 and won't run on Apple Silicon (ARM).  If your final production environment is Linux, your easiest route would be Docker on Linux.
For your more specific questions: 1) yes, those are the links to the ANTs and Niftyreg projects.  2) On NITRC, our "default" version is Linux native (without Docker). The "Docker" version should run on any x86/x64 but Linux is the only thing we've tested. I'm not aware of anyone running it on Windows. The mac version (native) will run on Mac. 3) Yes, both of those projects use CMake to build 4) In an ideal case cmake builds look something like-- cd folder/with/source/code # folder will contain CMakeLists.txt mkdir build cd build cmake .. make sudo make install and repeat for ANTs. 5) The distribution shouldn't really make a difference. Ubuntu should be fine and if it wasn't working on Ubuntu I'm sure someone would have reported it by now, but we are running Rocky Linux 8 (descends from Centos, which descends from Redhat). 6) Use the included run_mri_reface.sh script
Good luck! Chris Schwarz

Basic setup and usage for native Mac and Linux

Jesse Mahan — Tue, 26 May 2026 20:28:53 GMT

Hello, I am a total novice when it comes to using these types of programs. I have been in Windows IT support for two decades, so compiling things is not something I've ever needed to do; plus, very little Terminal use. I've been tasked with determining if MRI Reface can work for our use-cases, so I’m looking for help/direction on how to get these applications to function. I’m not a programmer or developer, so I’m really at a loss.
I'm attempting to first do a POC with the native 3.5 Mac version. Then, later, potentially having this run on a Linux EC2 using the native Linux 3.5 release.
We are using a Mac Studio M1 Max on Tahoe 26.5. I’ve installed MATLAB 2022a. Easy. Next steps: the Niftyreg and ANTS components.
#1 - Are these the best links to use for these components for this Mac?
Nifty reg: <a href="https://github.com/KCL-BMEIS/niftyreg">https://github.com/KCL-BMEIS/niftyreg</a>
ANTS: <a href="https://github.com/antsx/ants">https://github.com/antsx/ants</a>
 
#2 - Should different links be used if trying to set up the native Linux install? If so, which?
 
#3 – Am I right that I should be using CMake to compile both Nifty reg and ANTS?
 
#4 - I see the CMake text files in the Github data. Is this the best resource for which cmds to run? Are people using these successfully to compile and run the applications?
 
#5 - Is Ubuntu still the recommended Linux OS? Is there a release version that should be used or is known-good?
 
#6 – Once the Niftyreg and ANTS components are believed to be successfully ‘installed’, how do you run MRI Reface?
 
Thanks for any help you can provide or resources you can point me to.

RE: Resource recommendations

Paul Wright — Wed, 29 Apr 2026 15:19:45 GMT

Useful info, thank you. When I have more info after running an array of jobs I'll update the thread.
I agree there's probably an overhead to running in a singularity container.