I’ll defer to the software engineers for the first issue! For the second: does it work if you copy norm.mgz into orig/001.mgz? :-D
-- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Maya Yablonski <ma...@stanford.edu> Date: Tuesday, October 31, 2023 at 1:46 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs External Email - Use Caution Thanks! When I tried "recon-all -synthseg -subjid sub-xx -i <FILENAME>.nii.gz" I get an error that only says: ERROR: cannot use ML routines The same happened on an HPC cluster (linux) and on my local mac. I tried both Freesurfer 7.3.2 and 7.4.1. I have no issues running recon-all with defaults, and can also run mri_synthseg successfully. any ideas? are there any flags I need to add to my command? specify input/output folders? I defined a SUBJECTS_DIR that's not the default since I'm working on a shared system. As for fmriprep, the error I got was: "ERROR: no run data found in /PATH/freesurfer/sub-xx/mri. Make sure to have a volume called 001.mgz in /PATH/freesurfer/sub-xx/mri/orig." When I checked the folder, sub/mri had all the expected mgz files, but the orig subfolder was indeed empty. Many thanks for the help! Maya ________________________________ From: Maya Yablonski Sent: Monday, October 30, 2023 7:08 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Using Synthseg segmentations to fix recon-all outputs Hello, I am working with a pediatric sample for which we are seeing many segmentation errors using the standard recon-all pipeline (version 7.3.2). Running synthseg on the same input files improves the segmentations dramatically, and I would like to be able to fix the surface files (?h.white, ?h.pial) according to the synthseg segmentation. I could not find how to do this in the documentation? Can I place the synthseg.nii.gz file somewhere and rerun recon-all? or autorecon? Would appreciate any pointers to the right way to go about this! Alternatively, I ran recon-all-clinical and that also seems to work well on our data, however the output folder is not identical to the standard recon-all folder, so I can not use that with other preprocessing pipelines that rely on freesurfer output (e.g. fmriprep). I would appreciate any advice on how to leverage the synthseg outputs instead of manually editing the segmentations! Thank you, Maya
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