On 10/18/2022 11:29 AM, Young, Jenna M wrote:
External Email - Use Caution
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
- 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?
No, I had assumed that you had run recon-all on the volume and not just synthseg. If just synthseg, then you can run mri_segstats --seg synthseg.mgz --ctab-default --sum synthseg.stats
- 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.
Yes. The aseg.stats is generated from a completely different process and also includes some partial volume correction
- 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.
No, not now
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
You don't often get email from dgreve@mgh.harvard.edu. Learn why this is important https://secure-web.cisco.com/1oC-TVC6pzz0BIq_Dp0zRk6Fv-qcsATvQ8zB76fadpyzXRQNTdB6ycNuD2GJ40gSab90P2-WL324TdC6IIYhib_DNbANSsjZ5GrLa_HpStt0hsDYwUtre-UE7iO8EKY42FoQ6F7Dv1oFdDaFl1VyfxHLWRmCxEEEvfImGmemugttD5htF00fThXaW9DZwfkyEEnQLrUn_sxHHgqRKAM4wWBij10d3wVKz2qoP0FM1Stl24qKLmckdS_Pu4o-ngvqFM3UgcT_TZrSL3N3CN3bAlcaTLVPFpnRYyFZTRLp2yKYJp07k6tN4O9lrvbFvyAZ4/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification
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:
* External Email - Use Caution * 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1unKQJ15ZIRw0A1GsrnzZRqE39gklOr82SgHphPhUB5ghLM6KUdTudvq50_mDwhK3tjnLXW3ZD-IjuPmvz5IhpkxZbXirTai0eGclJScho_WDkphcwZdKMRaTq1cw4pkIr2EYIg9LzKThzEAETY68LnE3Q6QP7UzanUttOGKeFtYVgQL0xP890oWU45zu--h035PMwdjfeF57HZQMAsKTnUbo4i8pnUgL8GER98BCf4dd6RWnCb8ZrQcAkiSu7oDfTX2x92-sds65OWQXeDNhtbHpe4nnVDGiZHsB0yMExPjManzx9dlvyxaJ31lBIrDZ/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D05%257C01%257Cyoungjm%2540chop.edu%257Cc7e1b3ace9c04c8558f908daaf758eaf%257Ca611241607b041a59bb1d146b575c975%257C0%257C0%257C638015216708423779%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3D0SXXnjmhgC6kLuIAlldCTaSW6k9zmCzWXedfnbO6AGk%253D%26reserved%3D0>** This email originated from an EXTERNAL sender to CHOP. Proceed with caution when replying, opening attachments, or clicking links. Do not disclose your CHOP credentials, employee information, or protected health information to a potential hacker**.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer