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The specific volume to surface mapping we do in the HCP Pipelines minimizes the partial volume effects.

Matt.

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Marina Fernández marina.fdez.alvarez@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, May 28, 2021 at 10:06 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] PVC to calculate myelin maps

External Email - Use Caution Hi Matt,

Thank you very much for the quick answer.

We have our data analyzed with another pipeline that also uses Freesurfer functions. For this reason we prefer to calculate myelin maps outside of the HCP Pipelines.

Do you think the way of calculating the maps that I explained in the previous question is evenly valid?

Best wishes, Marina

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Glasser, Matthewhttps://secure-web.cisco.com/1EkIb4RUBbvp4aaCzTKvZqXi5mpWtbK6dEiwb2GFTBe5yhOUyifO_hV_E7W1QbzRQK0FwD5cE3KcRI74D3Ovox656ePedxamjtVAEW4AgL4A-7CpFTGP6z5Tq41NoOZ1ojD9zFUJk5ThErtAOajuSKZWvKvti9tqMIHF1q6hCwGlKHevaGmbXlNhh9Qy7R3bO5NIgNuF-fVDEzMvEnu0zjfgN_OsOBclQQKnAUOgbQN0YXzNIZrmOblbk3L2t_TpeCz4wAM71ypty2rwIPsMJYA/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Glasser%252C%2BMatthew%2522 Fri, 28 May 2021 07:34:15 -0700https://secure-web.cisco.com/1ljnBFwkQWFVBlnoXgh6utmDhvf7eskDl5mAoznGoGHO9FTeVRUYQtO-bfot3HqDYDehtfxbJhabnlcLwYGpH0dXP12Y55bVR65aMaKLBI2m5e3DpuIaGvkf3ceK3XJu0-ejvTaS0490ojIjr2iIxgGPOUX8HzFmINOe0OqACHWQa_U11JZn92WpectdOwu7kUNnLEJ1EEOKgypAFQnxBzkuHv-Esidv8bS9Fwbh--pHmipQ4dKxzOK4XeRnn2fte3bTthJQyxPdc-hxBj4-oqg/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20210528

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I would use the HCP Pipelines for this.

Matt.

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Marina Fernándezhttps://secure-web.cisco.com/1jnEmX8pyslFDNAKq1ESVKhaVYgavR5DWrZDCQVw6EIjIeRPu8VsMW2BmjjGD5q-TEhUnOvxdrLSTT5-Y6k0YXgDL7svI9z3nYXjvFbLZ7RTupBSGPm81_9ITZGgKJJOgPJdln72nUn8_i_M0BwX5vAQJhvU59P4tJ425dDyWnDLjXoT8Isqf8qqqez-ioXBS40q0Uny8MDDL0kBndUynxMfDLd8eLFxK2zhH_m6k3AE0fJN7n9AYbodo3QU0dDBjU5tlYbAcURsJL_uHxBtJ5Q/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Marina%2BFern%25C3%25A1ndez%2522 Fri, 28 May 2021 07:26:19 -0700https://secure-web.cisco.com/1ljnBFwkQWFVBlnoXgh6utmDhvf7eskDl5mAoznGoGHO9FTeVRUYQtO-bfot3HqDYDehtfxbJhabnlcLwYGpH0dXP12Y55bVR65aMaKLBI2m5e3DpuIaGvkf3ceK3XJu0-ejvTaS0490ojIjr2iIxgGPOUX8HzFmINOe0OqACHWQa_U11JZn92WpectdOwu7kUNnLEJ1EEOKgypAFQnxBzkuHv-Esidv8bS9Fwbh--pHmipQ4dKxzOK4XeRnn2fte3bTthJQyxPdc-hxBj4-oqg/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20210528

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Dear experts,

I want to calculate myelin maps using the ratio of T1w and T2w MRI images.

I saw that the correction of partial volume effects can be used to create

the maps (Shafee, Buckner & Fischl, 2015)*.

Can I use the PVC functions of PetSurfer for this purpose? And in case I

can:

Should I apply PVC only on T1? Or also in T2?

Which T1 should I use? The original T1 or the T1 with corrections (for

example, the nu.mgz file that is corrected for variations in intensity)?

Any other advice for calculating myelin maps would be welcome.

Thank you in advance,

Marina

*Link:

https://secure-web.cisco.com/1JlAz9aQioBCdg379E7idALB4EltLyOBrORvLMLOKKAfsOZ...

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