Re: [Freesurfer] FreeSurfer atlas and statistics question

2023-01-20 Thread Huang, Yujing 
Hi Jacob,

I hope this page will provide some information you are looking for - 
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation

BA/BA.thresh stats are computed with annotations created from a set of labels 
included in Freesurfer.

I think by default Freesurfer uses ?h.aparc.annot (Desikan-Killiany cortical 
atlas) to compute the stats.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Levman, Jacob
Sent: Friday, January 20, 2023 9:27 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FreeSurfer atlas and statistics question

To whom it may concern among FreeSurfer staff,

My colleagues and I have performed an analysis with FreeSurfer that is under 
peer review. The reviewer has asked that we detail each atlas relied upon and 
connect that with each of the statistics that we relied upon in our analysis.

The statistics that we relied upon were the .stats data from each of the 
following: aparc, aparc.DKTatlas40, aparc.a2009s, BA, BA.thresh, w-g.pct, curv, 
entorhinal_exvivo, wmparc, aseg.

Obviously we use the Desikan-Killiany-Tourville atlas (and aparc.DKTatlas40 
statistics were extracted from that atlas).
I know there are other atlases, such as the Destrieux atlas, etc., but I'm not 
certain which of the above codes were extracted from Destrieux, and which ones 
were extracted from other atlases (and the names of those other atlases).

We ran a recon-all command for this study, but we only used the statistics 
outlined above (aparc, aparc.DKTatlas40, etc.). We need a list of all atlases 
supported with recon-all, and which ones were relied upon to generate each of 
the statistics codes in the above list.

Perhaps there is a complete list on a website somewhere of all the atlases and 
which of these .stats codes came from which atlas, but my searches online have 
not revealed the appropriate website. Could someone answer this question, or 
direct me to a complete website with all these details?

Thanks so much for your assistance!

Jacob
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[Freesurfer] FreeSurfer atlas and statistics question

2023-01-20 Thread Levman, Jacob 
To whom it may concern among FreeSurfer staff,

My colleagues and I have performed an analysis with FreeSurfer that is under 
peer review. The reviewer has asked that we detail each atlas relied upon and 
connect that with each of the statistics that we relied upon in our analysis.

The statistics that we relied upon were the .stats data from each of the 
following: aparc, aparc.DKTatlas40, aparc.a2009s, BA, BA.thresh, w-g.pct, curv, 
entorhinal_exvivo, wmparc, aseg.

Obviously we use the Desikan-Killiany-Tourville atlas (and aparc.DKTatlas40 
statistics were extracted from that atlas).
I know there are other atlases, such as the Destrieux atlas, etc., but I'm not 
certain which of the above codes were extracted from Destrieux, and which ones 
were extracted from other atlases (and the names of those other atlases).

We ran a recon-all command for this study, but we only used the statistics 
outlined above (aparc, aparc.DKTatlas40, etc.). We need a list of all atlases 
supported with recon-all, and which ones were relied upon to generate each of 
the statistics codes in the above list.

Perhaps there is a complete list on a website somewhere of all the atlases and 
which of these .stats codes came from which atlas, but my searches online have 
not revealed the appropriate website. Could someone answer this question, or 
direct me to a complete website with all these details?

Thanks so much for your assistance!

Jacob
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.