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Hi Jocelyn,
Many thanks for your response. I just wanted to confirm a couple of things:
1. Could you advise what specific edits need to be made to the brainmask.mgz volume to fix the hole in the WM, i.e., do we need to add GM, delete GM? We are used to only editing the brainmask.mgz volume when there is an issue with the GM so just want to make sure that we are fixing this hole in the WM correctly. 2. If we are only interested in cortical thickness, surface area, volume and gyrification, can you confirm that we do not need to spend time editing issues around the ventricles?
Thank you in advance.
Harriet PhD Student | University of Bath
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of freesurfer-request@nmr.mgh.harvard.edu Sent: 10 November 2020 17:00 To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 201, Issue 15
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Today's Topics:
1. BIDS-ASL request for comments - closes THIS Friday (11/13) {Disarmed} (Franklin Feingold) 2. Re: Editing Issues (Mora, Jocelyn S.) 3. Create new .mgz from .annot (Hyon, Justin J.) 4. eddy_correct with DTI {Disarmed} (Wei Shao) 5. Correlation between thickness and csf_measures: vector (Steve Petersen) 6. color and sign of sig.mgh data (Rovai Antonin) 7. Postdoctoral Fellowship in advanced multi-parametric imaging in Parkinson?s disease, Alzheimer?s disease, and healthy aging (Maurizio Bergamino) 8. Re: Freesurfer 7.1.0 on CentOS 8.1 {Disarmed} (Snedden, Ali) 9. Re: trac-all -bedp error after successful -prep (Michele Valotti) 10. Re: Help with mergecontrasts-sess function (Paula Maldonado)
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Message: 1 Date: Mon, 9 Nov 2020 18:28:16 +0000 From: Franklin Feingold ffein@stanford.edu Subject: [Freesurfer] BIDS-ASL request for comments - closes THIS Friday (11/13) {Disarmed} To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: FA8577FC-D779-46BC-927D-79E95EE1BFEE@stanford.edu Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
The BIDS community is preparing to merge the ASL (Arterial Spin Labeling) extension. The updated draft is available for review at: https://secure-web.cisco.com/1ITF4bOtJJcQiVKXDz67qOkjGMsukmz9eyHDd76OIYTeEMN..., and comments and suggestions may be submitted on GitHub at: https://secure-web.cisco.com/1VL_oxffggPudlMHXkbtyOToPXYFpi9_8kZMHoiuC326KyV.... The community review will close on Friday (Nov 13) at 11:5 9pm PT (pacific time)
This BIDS extension seeks to establish how ASL data and additional metadata are organized within the BIDS structure. This encompasses the ASL sequences provided in the consensus paper [Alsop 2014], including single- and multi-time point pulsed and (pseudo)-continuous ASL.
The final review entails a two week period for public commenting, with a possibility of extension for unresolved discussion. Once public comments are concluded, there will be a one week freeze, during which only critical issues will be considered. (For more details on the release protocol, see https://secure-web.cisco.com/1A8qnp7KY-M8xxjfEiWTabhYuW0g9mTh5DrlGyQ6pc4EAyS...)
We look forward to hearing your feedback!
The BIDS Team