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Hi all
I'm following up on a previous report from May of 2021 that seemed to have the
same issue. When running an MP2RAGE (7T, 0.65mm isotropic, pTx), I got the
following error using recon-all -all -hires that seemed line one that Corinna
did:
Dear Doug et al
I was doing some cross-subject label morphing over a bunch of subjects (a big
continuous patch of vertices) and was having problems with quite a number of
'missing' vertices in the morphed label.
I saw Doug's previous response to this on the message board that there was a
dev
Dear Doug et al.,
is there a hidden option (perchance) to get bootstrapped estimates of the
correlation coefficients/regression parameters in qdec?
cheers
Fred
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Hi Doug
sorry to nudge - any thoughts on lta tweaking?
cheers,
Fred
On 30 Apr 2013, at 16:44, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Fred,
I'll have to defer to Doug on this
Bruce
On Tue, 30 Apr 2013, Fred Dick wrote:
Hi Bruce
On 30 Apr 2013, at 13:36, Bruce Fischl
a
new lta? Is the only difference between the lta files the matrix? Or did the
src and dst geometry and/or type change?
doug
On 05/02/2013 05:52 AM, Fred Dick wrote:
Hi Doug
sorry to nudge - any thoughts on lta tweaking?
cheers,
Fred
On 30 Apr 2013, at 16:44, Bruce Fischl fis
still have an outstanding question?
doug
On 05/02/2013 12:55 PM, Fred Dick wrote:
Hi Doug
totally no worries (this hardly counts as a delay!).
I'm running it as
tkregister2 --ltaout tal-out.lta --gca [sub] --check-reg
As you had suggested, the source and dst are switched
with Fred?
doug
On 05/02/2013 01:13 PM, Fred Dick wrote:
Yes - maybe it is an idiotic one, but is there a straightforward way to
write out a tkregister-tweaked talaiarch.lta with the correct geometry so
that mri_ca_normalize/register will read it right?
On 2 May 2013, at 18:04
was the inverse transform of what I
thought it was, e.g., sub = standard).
So I'm slightly stymied.
Thanks tons,
Fred
On 29 Apr 2013, at 15:06, Fred Dick ubjt...@mail.bbk.ac.uk wrote:
Aha, I shall quickly try with the non -w weighting and see what happens.
Thanks!
On 29 Apr 2013, at 15
/freesurfer-5.0.0-cent4-64/average/RB_all_2008-03-26.gca \
label_means.mgz
mri_convert -nth 1 \
/usr/local/freesurfer-5.0.0-cent4-64/average/RB_all_2008-03-26.gca \
labels.mgz
cheers
Bruce
On Tue, 30 Apr 2013, Fred Dick wrote:
Hi again
different weighting sorta kinda worked better
Dear all
I'm having difficulties getting correct Talairach.lta's from synthetic flash
volumes (Bruce, you are probably sorry you ever told me about this!).
Basically the brain is over-scaled (bigger than it should be), which I think is
happening because the contrast is so good (gm much darker
we don't have much experience with this. Which synthesis are you using? You
might need to use a different one for the talairaching to more closely match
the atlas (maybe a TR=20,TE=2.5,flip=20-30 one)
On Mon, 29 Apr 2013, Fred Dick wrote:
Dear all
I'm having difficulties getting
realizable in an real
MR acquisition. Not surprising that the tal stuff fails
On Mon, 29 Apr 2013, Fred Dick wrote:
Hi Bruce
I'm using TR=20, flip=30, TE=5 - but possibly irrelevant as also have the -w
flag on.
I originally thought this was from a bad brainmask, but then generated a
good
setting -n 0 in mris_make_surfaces to it runs for 0
iterations. Or we can put something together to create area - it should be
trivial
cheers
Bruce
On Mon, 15 Apr 2013, Fred Dick wrote:
Hi there
[Doug/Bruce, sorry for storm of enquiries!]
V quick question: I've fixed up some small
On 15 Apr 2013, at 17:58, Douglas Greve gr...@nmr.mgh.harvard.edu wrote:
Hi Fred, why do you want to save it as a wfile? We're trying to phase wfiles
out. Can you use mgh format?
doug
On 4/15/13 12:56 PM, Fred Dick wrote:
Hey again
sorry, I seem not to be able to accomplish this very
Dear all
I have been trying to recon a high-res (.75 isotropic) volume, which goes
along fine until it hits a certain bit of mri_ca_normalize. I've run this
4 times and it always dies at the same point.
There was also a previous unanswered post about 8 months ago showing an
error at the same
Hi Thomas et al.,
I finally had luck with swapping over to XQuartz (2.7.0) - now the number
and depth of colors is back to normal.
cheers,
Fred
Hi, was this problem ever resolved?
I am seeing the same issue on my mac desktop.
Thanks,
Thomas
On Mon, May 10, 2010 at 3:47 AM, Fred Dick
Dear all
we have had some odd behavior in 4 fairly high quality datasets that have been
very nicely normalized and deskulled with a good Talairach but then only half
filled in wm.mgz and all surfs (to various semi-planes). Orientation seems
correct in tkmedit as well. We were thinking that it
that is at fault.
cheers,
Bruce
On Tue, 12 Apr 2011, Fred Dick wrote:
Dear all
we have had some odd behavior in 4 fairly high quality datasets that have
been very nicely normalized and deskulled with a good Talairach but then
only half filled in wm.mgz and all surfs (to various semi
Dear all
This is a pretty minor issue (except for figure making) - but has anyone
experienced and then fixed a display problem in tksurfer/tkmedit in OSX 10.6
(possibly also 10.5) where graphics seem to be drawn only with 256 colors,
thereby giving images a kind of contour-plot look? (See
. tksurfer/tkmedit display color fix in OSX 10.6? (Fred Dick)
--
Message: 1
Date: Sun, 9 May 2010 15:34:35 +0100
From: Fred Dick fd...@crl.ucsd.edu
Subject: [Freesurfer] tksurfer/tkmedit display color fix in OSX 10.6
, Fred Dick wrote:
Dear Bruce et al.,
I noticed a while back that there was a thread on local distortions
(too much stretching + curlicues) popping up after mris_sphere;
we've seen similar things, and thus far haven't been able to fix
them by tweaking options. Is there any update
Hi Bruce, Doug, et al.
I was going to pick up some machines for freesurfer recon purposes -
any recommendations on preferred platform?
cheers,
Fred
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