On 6/5/2020 3:54 PM, Sneha Pandya wrote:
External Email - Use Caution
Dear Dough,
Is samseg2recon run by default when we run just samseg command? After
samseg is completed it displays towards the end samseg2recon run time
in sec and hours, right before computation time of samseg as below. If
it is called by samseg command itself there would be no need to run
samseg2recon separately after samseg command right unless it is doing
something in addition?
Started at Fri Jun 5 12:49:50 EDT 2020
Ended at Fri Jun 5 12:51:57 EDT 2020
Samseg2recon-Run-Time-Sec 127
Samseg2recon-Run-Time-Hours 0.04
samseg2recon Done
Started at Fri Jun 5 12:27:43 EDT 2020
Ended at Fri Jun 5 12:51:57 EDT 2020
Samseg-Run-Time-Min 24.23
Samseg-Run-Time-Hours 0.40
it is not run by default.
I had ran few subjects with samseg from Freesurfer dev version in Oct
of 2019 and compared it with samseg version from Freesurfer v7.1.0 and
realized that some file names are different. Samseg from dev version I
ran in 2019 created file t1w_biasCorrected.nii, t1w_biasField.nii,
t1w_crispSegmentation.nii names under saubject/mri/samseg directory
and Freesurfer v7.1.0 creates mode01_bias_corrected.mgz,
mode01_bias_field.mgz, seg.mgz files. I assume these files should be
comparable across these two versions right? Also, I do not see
seg.stats file when I ran with dev version in 2019. Which stat file am
I suppose to consider in lieu of seg.stats file when I ran with 2019
dev version?
Yes, a lot of file names changed. You should look at the seg.stats file
Besides, when we ran samseg in 2019 we had used mri/T1.mgz file as an
input. Will this be a problem based on your suggestion in
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65310.html
Thank you,
Sneha
*From: *Douglas N. Greve <mailto:dgr...@mgh.harvard.edu>
*Sent: *Tuesday, May 5, 2020 11:38 AM
*To: *freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *[EXTERNAL] Re: [Freesurfer] samseg with subfields
In theory it is possible, though I don't know if it is better or
worse. You can run samseg, then run samseg2recon (this creates a
folder that looks like it was created by recon-all), then run
subfields on that folder
On 5/5/2020 10:45 AM, Sneha Pandya wrote:
* External Email - Use Caution *
Dear experts,
I want to revisit if anyone has ran subfield analysis just by
running samseg? If it is possible is it as reliable as from
running regular routine with “-all” recon-all flag?
Thank you,
Sneha
*From:* Sneha Pandya
*Sent:* Thursday, April 30, 2020 4:15 PM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* samseg with subfields
Dear experts,
Is it possible to run subfield analysis (hippcampal subfields,
amygdalar, thalamic nuclei, and brainstem structures) when we only
run samseg on our dataset?
Thank you,
Sneha
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt from
"urldefense.proofpoint.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwMD-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=AEsux002jQ5JzIPYIcsXKAuQmrt-1dubP8ZVldIiOrE&m=ZcRwF0g_TOQUS7q9Ip9PNRLVW7xP32AuzLy27Bqt7sU&s=1JOezYk0f3Rm2CGmy4t2lDlZRmpNqY-iPUnty5HzLro&e=>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
