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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