External Email - Use Caution
I re-ran the affected subjects on the Linux workstation and the outputs are good, no artefacts. The problem may have been related to the MacOS.
Thank you so much for the help.
On Tue, Jan 13, 2026 at 11:10 AM fsbuild fsbuild@contbay.com wrote:
External Email - Use CautionWondering now what version of MacOS you are running. While Freesurfer 8.1.0 was not tested on MacOS Tahoe (26.X), we’ve noticed that some mri_synth* commands did not always work correctly on the older MacOS Monterey (12.X) and Ventura (13.X) systems. At least for FS 8.1.0, we saw some of those commands run more successfully on macOS Sonoma (14.X) and Sequoia (15.X), presumably from bug fixes and updates, including GPU performance. Please let us know if you find the output is markedly different on Linux compared to (a specific version of) MacOS.
- R.
On Jan 13, 2026, at 00:09, Tejendra Singh tejendra.singh.cp@gmail.com wrote:
External Email - Use CautionThank you for the suggestion. To clarify, the white block artefacts are present in the saved SynthSR NIfTI output itself, not just during visualization. I observe the same rectangular regions when opening the output in multiple viewers (e.g., Freeview, MRIcron), and they persist after reloading the file.
For context, I am running: OS: macOS (Apple Silicon); System: MacBook Air (M-4); FreeSurfer: 8.1.0 (arm64 build); Graphics: Integrated Apple GPU; SynthSR command: mri_synthsr (default model and also tested with --lowfield)..
I will try re-running one of the affected subjects on a different system (Linux workstation) and compare the SynthSR output to see if the artefact reproduces. I will report back once I have tested this.
Thanks again for the helpful suggestion..
On Mon, Jan 12, 2026 at 1:35 PM fsbuild fsbuild@contbay.com wrote:
External Email - Use CautionI’m wondering if this is a graphics issue causing the screen not to update properly, related to the fact that you are using T1 images. You could try one of the subjects that displays the erroneous output on a different system and see if you get the same result. Maybe you could let us know what the system is you are running on including the OS and what your graphics hardware is.
- R.
On Jan 12, 2026, at 00:57, Tejendra Singh <tejendra.singh.cp@gmail..com> wrote:
External Email - Use CautionThis is the issue
On Mon, Jan 12, 2026 at 11:25 AM Tejendra Singh < tejendra.singh.cp@gmail.com> wrote:
Hello everyone, I am using SynthSR (FreeSurfer 8.1.0, mri_synthsr) to standardize T1-weighted MRI scans across a multi-protocol clinical dataset. The majority of subjects process correctly; however, for a small subset of scans, the SynthSR output contains prominent white rectangular/block artefacts over the brain volume.
Key observations:
The artefacts are not present in the original T1 images
They appear only in the SynthSR output
The affected original scans are already 1 × 1 × 1 mm isotropic
Original images otherwise appear visually normal (no obvious truncation or corruption)
Artefacts look axis-aligned (rectangular slabs), suggesting a reconstruction failure rather than anatomy
Example workflow:
mri_synthsr \ --i sub-XX_T1w.nii \ --o sub-XX_synthsr.nii.gz
*Questions:*
Are these white block artefacts a known failure mode of SynthSR for certain inputs? 2.
Are there recommended preprocessing checks (e.g., header/orientation fixes) to reduce this issue? 3.
Would trying the --v1 model be advisable in such cases? 4.
If the original scan is already clean and isotropic, is it methodologically acceptable to exclude SynthSR output and retain the original image for downstream processing?
I am currently treating SynthSR as an exploratory preprocessing step and excluding affected subjects from the SynthSR-based pipeline, but I would appreciate guidance on best practices.
Thank you for any insights
<Screenshot 2026-01-12 at 11.26.45 AM.png>
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