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Hi Douglas,

 

Thanks for your response. I have a few follow-up questions

 

> If you want recon-all type stats, you can run synthseg storing the output in subject/mri, then look at the recon-all.log file

 

1. Should the recon-all.log file be generated by mri_synthseg by default? If not, how should I instruct mri_synthseg to produce the log file?

 

2. Are there any significant differences between the measures in volumes.csv produced by mri_synthseg and the measures in aseg.stats? I have figured out how to extract the measures from volumes.csv and map them to the volumetric measures from aseg.stats, but if the measurements are actually measuring different information that would be good to know.

 

3. Is there a way to use a custom/alternative segmentation file in the recon-all pipeline? I thought I had read something indicating this was possible, but I cannot seem to find that info on the wiki if it is possible.

 

Thanks for your help.

Best,

Jenna

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, October 16, 2022 at 8:54 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [External]Re: [Freesurfer] Getting recon-all stats from SynthSeg 2.0 segmentations

 

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we don't have a way to do this yet. If you want recon-all type stats, you can run synthseg storing the output in subject/mri, then look at the recon-all.log file to get the mri_segstats command that creates the aseg.stats file, modify the command line to use the synthseg output and change the .stats file name

On 10/4/2022 9:42 AM, Young, Jenna M wrote:

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Hello all,

 

I'm trying to perform a comparison of the global and regional phenotype statistics produced by `recon-all` with the outputs of SynthSeg 2.0. Based on the wiki, it looks like I should be able to pass the segmentation from SynthSeg to recon-all (somehow) and run it through steps further down the pipeline.

 

My current best guess at a command to do this is:

 

recon-all -autorecon2-pial -autorecon3 -s SUBJECTID  -i INPUT_IMAGE.nii.gz

 

At this point, I have 2 questions:

1. Is -autorecon2-pial the correct step to insert the SynthSeg segmentations into the recon-all pipeline?

2. What is the correct way to pass an existing segmentation file to recon-all, and how do you also pass it the original brain image?

 

Thanks in advance for your suggestions.

 

Jenna

 

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