Correct, the stable version has the same (adult only) functionality as before.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Alexopoulos, Dimitrios
Sent: Thursday, September 17, 2020 1:42 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Trac
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OK. Sorry for confusing with the infant pipeline.
As it relates to the adult stable release package 7.1.1, if we want tracts
using this release we should be using the tracula.beta separately, not the
tracula version in the stable release?
In other w
The beta is the only tracula version with infant processing options (which as
you know are currently under development 🙂).
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Alexopoulos, Dimitrios
Sent: Thursday, September 17, 2020 1:22 PM
To: Freesurfer
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We need to analyze some pilot 2yo datasets and need tracts.
We 'd like to use FS7, which is giving us better surfaces on the 2yo's than the
current infant FS release.
To clarify, if we wants tracts using the stable FS7.1 release, we should using
the
Yes, same. Just FYI, the only "unstable" part of the 7.1.tracula.beta is the
tracula part, everything else is from the stable release. But it would only
make sense to use if you want to try out the newer features.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on
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Thx Anastasia. I prefer to use the stable releases. So the same
diiffusion/tracula inputs for FS 7 as FS 6, for example\
using a generic dmrirc parameter file ?
Best.
Jim
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Yendiki, Anastasia
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Right I would recommend pre-scan normalize on for all images being acquired in
a study. There are important considerations for fMRI, diffusion, and ASL (and
even auxiliary scans like SE fieldmaps) not just T1w/T2w/FLAIR. That said, I
was guessing t
I would guess it is pretty important for a 12 channel also, although it depends
on field strength and also needs a body coil transmit to be maximally
effective. In general we use it whenever we can
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Glasser, Matthew
Sent: T
I agree. The 8 channel coils can be trouble as they usually don’t have very
good SNR at the vertex, so you are likely to see a lot of variance in the
results in those regions
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Glasser, Matthew
Sent: Thursday, September 17,
And more details about the study would also help. What field strength? Was the
transmit coil a body coil? In the end though I’m not sure we are going to be
able to give you an answer as it is an empirical question as to whether
including them increases your variance more than it increases your p
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Maybe Bruce or Doug wants to comment but probably if you are using a 12CH coil
it isn’t so important to have on. It’s pretty much required for a 32CH coil,
as the bias field is quite fast.
Matt.
From: on behalf of "Mikolas, Pavol"
Reply-To: Free
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Dear Matthew,
thank you for this important point. I will check this. There might be just a
few subjects with 8 and 32 head coil, so that it should be possible to discard
them without affecting the sample size too much.
Do you think, you could give u
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That alone will be a huge factor in variable SNR (and receive field). Head
coils are not interchangeable like that.
Matt.
From: on behalf of "Mikolas, Pavol"
Reply-To: Freesurfer support list
Date: Thursday, September 17, 2020 at 7:22 AM
To: 'Fr
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Hi,
I have a question regarding the flag -- inittp 0 (no init ) in
mri_robust_template. What does ‘no init’ mean in this context and which
consequences arise from using this flag?
Thank you!
Best,
Marisa
___
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Dear Matt,
unfortunately we have no highres T2w or FLAIR.
In this multicentric study, we tended to use the 12 head coil. However, some
centers used a 8 or a 32 head coil.
Thanks
Pavol
Von: freesurfer-boun...@nmr.mgh.harvard.edu
Im Auftrag von Gl
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What head coil did you use? Do you have a highres T2w or FLAIR?
Matt.
From: on behalf of "Mikolas, Pavol"
Reply-To: Freesurfer support list
Date: Thursday, September 17, 2020 at 7:12 AM
To: "'freesurfer@nmr.mgh.harvard.edu'"
Subject: [Freesurfer
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Dear Freesurfer Developers,
I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using
Freesurfer. I found out, that most of the scans were performed with the
'prescan normalize' option. However, by approx.. 12 % of participants, th
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Thank you very much Prof Greve! I'm almost done! Now, using mri_volcluster
I can identify the vertex number with highest significance within a ROI in
a surface sig.mgh map (see attached txt). However I don't know how to
compute the corresponding MNI coo
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