Hi, quick question
I'm just going to rerun these without the -T2 stuff for now so I can get
going on analysis.
What stages of recon-all do I have to run to fix everything the -T2pial
mishap broke? The process flow tables on the website seem a bit out of date.
mw
On Sat, Sep 28, 2013 at 3:24 PM
hmmm, maybe Nick or Doug can investigate, although we are crazy busy at
the moment
On Sat, 28 Sep 2013, Michael Waskom wrote:
>
> On Sat, Sep 28, 2013 at 5:28 AM, Bruce Fischl
> wrote:
> hmmm. That would be strange and would result in complete failure
>
>
> I agree, but
>
> $ grep bbre
On Sat, Sep 28, 2013 at 5:28 AM, Bruce Fischl wrote:
> hmmm. That would be strange and would result in complete failure
I agree, but
$ grep bbregister recon_log_withT2.txt
$ grep fslregister recon_log_withT2.txt
both turn up empty
___
Freesurfer mail
r
to modify the –nsigma_above and -nsigma_below flags for
mris_make_surfaces when using -T2pial?
Peace,
Matt.
From: Michael Waskom
Date: Friday, September 27, 2013 2:20 PM
To: Matt Glasser
Cc: Bruce Fischl ,
"Freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Major
Date: Friday, September 27, 2013 10:06 PM
To: Matt Glasser
Cc: Bruce Fischl ,
"Freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Major problems with T2-based pial removal
Hmm, Ok. Thanks Matt.
I still think it's weird that the T2 didn't seem to ever get registered to
s_make_surfaces when using -T2pial?
>
> Peace,
>
> Matt.
>
> From: Michael Waskom
> Date: Friday, September 27, 2013 2:20 PM
> To: Matt Glasser
> Cc: Bruce Fischl , "
> Freesurfer@nmr.mgh.harvard.edu"
> Subject: Re: [Freesurfer] Major problems with T2-b
eesurfer] Major problems with T2-based pial removal
Hi Matt,
It's this sequence:
http://cni.stanford.edu/wiki/MR_Protocols#T2_weighted_scans (the 3D T2)
You can click the console screenshots for a closer view of the parameters --
let me know if you need me to track down more info.
mw
On
Hi Matt,
It's this sequence:
http://cni.stanford.edu/wiki/MR_Protocols#T2_weighted_scans (the 3D T2)
You can click the console screenshots for a closer view of the parameters
-- let me know if you need me to track down more info.
mw
On Fri, Sep 27, 2013 at 11:38 AM, Matt Glasser wrote:
> Som
Someone sent me a different kind of T2w image and it didn't work so well,
so we need to know what kind of image this is.
Peace,
Matt.
On 9/27/13 1:33 PM, "Bruce Fischl" wrote:
>nope, pretty much only with T2-space with and without a flair pulse
>On Fri,
>27 Sep 2013, Matt Glasser wrote:
>
>>
nope, pretty much only with T2-space with and without a flair pulse
On Fri,
27 Sep 2013, Matt Glasser wrote:
> Also, what kind of T2w sequence is this? I think we've mostly tested it
> with the T2-SPACE (unless Bruce has tested with other things).
>
> Peace,
>
> Matt.
>
> On 9/27/13 12:58 PM, "B
Also, what kind of T2w sequence is this? I think we've mostly tested it
with the T2-SPACE (unless Bruce has tested with other things).
Peace,
Matt.
On 9/27/13 12:58 PM, "Bruce Fischl" wrote:
>Hi Michael
>
>that looks pretty bad! What is the resolution of the T2? The T1 that you
>overlay on al
Hi Michael
that looks pretty bad! What is the resolution of the T2? The T1 that you
overlay on also looks somewhat blurry - what was it?
Bruce
On Fri, 27 Sep
2013, Michael Waskom wrote:
Hi, just to make the problem a bit more transparent, I took a second
screenshot of the slices with the
Hi, just to make the problem a bit more transparent, I took a second
screenshot of the slices with the pial surface from the -T2pial run in red
and the pial surface from the normal run in cyan:
https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png
On Fri, Sep 27, 2013 at 10:37 AM, Mich
Hi,
I'm using FS 5.3 and trying to use hires T2-weighted scans to refine the
pial mesh.
However, I've found that using the T2 is causing rather dramatic problems
with the pial surface.
I processed the same subject's data with and without the -T2pial option.
Here are links to a) pial surface imag
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