Great, thanks!
BTW, Doug, your primer on the hell of transformation matrices is very nice.
On 2 May 2013, at 18:19, Douglas N Greve wrote:
>
> Funny you should mention that. Martin just wrote a program to convert lta's
> from one type to another. Martin, can you share with Fred?
> doug
>
>
Funny you should mention that. Martin just wrote a program to convert
lta's from one type to another. Martin, can you share 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 talaiar
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, Douglas N Greve wrote:
> Hi Fred, so do you still have an outstanding
Hi Fred, so do you 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 a
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 (in talaiarch.lta, the
.gca is the dst, whereas in new output file, it's the src).
Also, the RB...gca
Hi Fred, sorry for the delay. How are you running tkregister2 to produce
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 twea
Hi Doug
sorry to nudge - any thoughts on lta tweaking?
cheers,
Fred
On 30 Apr 2013, at 16:44, Bruce Fischl 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 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 wrote:
>
>> Hi Fred
>>
>> I know it's a silly question but are you sure that file exists and is
>> readable by you? The fact that it's calling GCAread
Hi Bruce
On 30 Apr 2013, at 13:36, Bruce Fischl wrote:
> Hi Fred
>
> I know it's a silly question but are you sure that file exists and is
> readable by you? The fact that it's calling GCAread means it's doing the
> right thing and support gca files.
Totally not a silly question. With tkreg
Hi Fred
I know it's a silly question but are you sure that file exists and is
readable by you? The fact that it's calling GCAread means it's doing the
right thing and support gca files. You can also extra the mean of the
highest prob label (-nth 0) and the label itself (-nth 1) using
mri_conve
Hi again
different weighting sorta kinda worked better. It might be a dud brain.
But on this topic - I realized I wasn't quite sure of a couple of things, and
had some errors pop up with some tkregister2 options.
[btw, running stable 5.2.0 on snow leopard]
1) I first tried to check the reg t
Aha, I shall quickly try with the non -w weighting and see what happens.
Thanks!
On 29 Apr 2013, at 15:05, Bruce Fischl wrote:
> yes, the -w will create an optimal weighting to maximize gray/white contrast.
> The image it generates won't in general be physically realizable in an real
> MR acq
yes, the -w will create an optimal weighting to maximize gray/white
contrast. The image it generates won't in general be physically
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 -
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
one and same thing happening.
On 29 Apr 2013, at 14:27, Bruce Fischl wrote:
> Hi Fred
>
> we don't have much exper
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
Hi Fred
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
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