External Email - Use Caution
I’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(a)gmail.com> wrote: External Email - Use Caution This is the issueOn Mon, Jan 12, 2026 at 11:25 AM Tejendra Singh <tejendra.singh.cp(a)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 imagesThey appear only in the SynthSR outputThe affected original scans are already 1 × 1 × 1 mm isotropicOriginal images otherwise appear visually normal (no obvious truncation or corruption)Artefacts look axis-aligned (rectangular slabs), suggesting a reconstruction failure rather than anatomyExample workflow:mri_synthsr \
--i sub-XX_T1w.nii \
--o sub-XX_synthsr.nii.gzQuestions:Are these white block artefacts a known failure mode of SynthSR for certain inputs?Are there recommended preprocessing checks (e.g., header/orientation fixes) to reduce this issue?Would trying the --v1 model be advisable in such cases?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>_______________________________________________Freesurfer mailing list -- freesurfer@nmr..mgh.harvard.eduTo unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/