AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
Why are you registering it to the MNI prior to FS analysis?
On 1/26/2021 10:13 AM, Trisanna Sprung-Much wrote:
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Hi Doug and Matt
So the HCP scans are at 0.5mm
PM
To: Freesurfer support list
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
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Hi Matt
Great, I will check out all the folders. Just made an account now.
By "paint surfaces" I mean create/edit labels on the surfaces, specifically
related
urfer-boun...@nmr.mgh.harvard.edu
on behalf of Glasser, Matthew
Sent: Tuesday, January 26, 2021 3:06 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
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Sorry I’m completely confused now about what you are trying to do. T
0,0,0). What does “paint surfaces” mean anyhow?
Matt.
From: on behalf of Trisanna
Sprung-Much
Reply-To: Freesurfer support list
Date: Tuesday, January 26, 2021 at 1:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
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McGill University
MD Anderson Cancer Centre
--
From: on behalf of "Glasser, Matthew"
Reply-To: Freesurfer support list
Date: Tuesday, January 26, 2021 at 1:57 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
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: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
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Hi Bruce
Thanks for your speedy response. This would be an immense time saver if this
works. I will give this a go.
Yes, you are correct about the blurring as well!
Best
Trisanna Sprung-Much
Research Associate
McGill
Sure. Give it a try and if something fails we can see about fixing it
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Trisanna Sprung-Much
Sent: Tuesday, January 26, 2021 1:24 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
Centre
--
From: on behalf of "Fischl, Bruce"
Reply-To: Freesurfer support list
Date: Tuesday, January 26, 2021 at 1:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
Hi Trisanna
Yes, I’m pretty sure that would work. That is, using t
...@nmr.mgh.harvard.edu
On Behalf Of Trisanna Sprung-Much
Sent: Tuesday, January 26, 2021 1:13 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
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Hi Matt
OK, I think there has been some confusion and I think I just realized
January 26, 2021 at 11:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
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I think it would be a good idea to take a step back and tell us what you are
trying to accomplish. This is all not the right way to go about th
: on behalf of Trisanna
Sprung-Much
Reply-To: Freesurfer support list
Date: Tuesday, January 26, 2021 at 9:45 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
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Hi Matt
The sole purpose of
] HCP T1w scans on FreeSurfer 7.1
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That’s not a good idea either.
Matt.
From: on behalf of "Douglas N. Greve"
Reply-To: Freesurfer support list
Date: Tuesday, January 26, 2021 at 9:30 AM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject:
.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Tuesday, January 26, 2021 11:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
Why are you registering it to the MNI prior to
the subject’s own physical space.
Matt.
From: on behalf of Trisanna
Sprung-Much
Reply-To: Freesurfer support list
Date: Tuesday, January 26, 2021 at 9:53 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
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Hi Matt
nmr.mgh.harvard.edu>
on behalf of Douglas N. Greve
<mailto:dgr...@mgh.harvard.edu>
Sent: Monday, January 25, 2021 11:22 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] HCP T1w scans o
ry 25, 2021 11:22 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
You don't need any special flags with the -hires option. Also, it is
helpful to include the recon-all.log file.
On 1/22/2021 12:15 AM, Glasser, Matthew wrote:
Exte
: Freesurfer support list
Date: Tuesday, January 26, 2021 at 9:13 AM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
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Hi Doug and Matt
So the HCP scans are at 0.5mm resolution because they were originally 0.7mm
Best
Trisanna
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Monday, January 25, 2021 11:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
You don't need any special flags with
sanna
Sprung-Much
*Reply-To: *Freesurfer support list
*Date: *Thursday, January 21, 2021 at 12:21 PM
*To: *Freesurfer support list
*Subject: *Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
**
**
*External Email - Use Caution *
Hi there
As a follow-up to this question, I trie
:05 PM
To: Freesurfer support list
Subject: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
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Hi there
If I want to run some HCP subjects that are 0.5mm iso T1w scans (MPRAGE) in
FreeSurfer 7.1, would I simply use the following flags, or am I missing
something
: Freesurfer support list
Subject: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
External Email - Use Caution
Hi there
If I want to run some HCP subjects that are 0.5mm iso T1w scans (MPRAGE) in
FreeSurfer 7.1, would I simply use the following flags, or am I missing
something?
-3T -MPRAGE
External Email - Use Caution
Hi there
If I want to run some HCP subjects that are 0.5mm iso T1w scans (MPRAGE) in
FreeSurfer 7.1, would I simply use the following flags, or am I missing
something?
-3T -MPRAGE -hires
Do we need an expert file with version 7.1 to specify the nu
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