External Email - Use Caution        

Hello Douglas,

Thank you for your advice.

As you have suggested, I have now used orig.mgz from the recon-all longitudinal processing stream as an input to Samseg longitudinal processing stream. For comparison, I have the following volumes

1) Left-Hippocampus volume from recon-all longitudinal processing stream in aseg.stats (3321.5, mm^3)

2) Left-Hippocampus volume from samseg longitudinal processing stream in samseg.stats (3660.103030, mm^3)

3) Left-Hippocampus volume from longitudinal Hippocampal subfields processing stream in lh.hippoSfVolumes-T1.long.v21.txt (Whole_hippocampus 3012.029850, mm^3; Whole_hippocampal_body 999.162202, mm^3; Whole_hippocampal_head 1581.449339, mm^3; Hippocampal_tail 431.418310, mm^3)

When I visually check, the Left-Hippocampal segmentation appears to be better from recon-all longitudinal processing stream. There appears to be a slight overestimation with samseg longitudinal processing stream.

Question 1) Additionally, the longitudinal Hippocampal subfields processing stream gives another set of volumes. Which set of Left-Hippocampal subfields volumes would correspond to Left-Hippocampal volume from recon-all longitudinal processing stream?

Question 2) If i want to analyse the Hippocampal subfields volumes, would it make sense to correct for ICV from the samseg longitudinal processing stream or the hippocampal volume from recon-all longitudinal processing stream?

BW

Jay

On Mon, Feb 22, 2021 at 4:14 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

On 2/18/2021 7:06 AM, Jayachandra Raghava wrote:

        External Email - Use Caution        

Hello Freesurfer Experts,

I am using Freesurfer version 7.1.1 to perform longitudinal Samseg processing (using run_samseg_long) on my T1 longitudinal data.

1) First, I run the mri_robust_template to generate the mean.mgz using T1.mgz from the cross sectional recon-all pipeline. Would it be better to use T1.mgz from the longitudinally processed data?

You mean the T1.mgz from the recon-all output? Don't use that. Use the orig.mgz.from the long stream (you'd only need to run it long enough to produce the orig.mgz)

2) There are few subjects who do not have followup data. How do I process these subjects to avoid the bias introduced by the longitudinal Samseg pipeline?

You can run the recon-all long stream on that one time point;  it will apply a registration designed to not introduce bias, then use the orig.mgz

3) For the same subject, I see that the subcortical volumes from longitudinal recon-all pipeline from aseg.stats (e.g Left-Hippocampus volume is 3321.5mm3) are different to the subcortical volumes from longitudinal samseg pipeline from samseg.stats (e.g Left-Hippocampus volume is 3899.628686mm3). Which of these measures would be recommended?

In general I would say samseg, but that is a pretty big difference. Can you take a look and see if one looks better than the other?

Thank you very much for your support!

Best wishes

Jay

_______________________________________________
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

_______________________________________________
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

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer