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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
Dear Maya, You can use then -synthseg flag with recon-all to use SynthSeg instead of the standard algorithm 😉 For fmriprep: which is the offending volume? There are very minor differences with the standard recon-all output. Cheers, /E
-- Juan Eugenio Iglesias http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Maya Yablonski mayay@stanford.edu Date: Monday, October 30, 2023 at 1:09 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs
External Email - Use Caution 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
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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Maya Yablonski mayay@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
Can you try to set environment variable FS_ALLOW_DEEP before running 'recon-all -synthseg'.
If you are using tcsh or csh, do 'setenv FS_ALLOW_DEEP 1'.
If you are using bash, do 'export FS_ALLOW_DEEP=1'.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Iglesias Gonzalez, Juan E. Sent: Tuesday, October 31, 2023 5:17 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Maya Yablonski <mayay@stanford.edumailto:mayay@stanford.edu> Date: Tuesday, October 31, 2023 at 1:46 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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
freesurfer@nmr.mgh.harvard.edu
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Huang, Yujing -
Iglesias Gonzalez, Juan E. -
Maya Yablonski