Doug,
The file "segmentation.mgz" doesn't exist.
I think that you mean that segmentation.mgz stands
for either WM or GM. Can you provide me the
exact file names of the final WM and GM segmentations.
Ed
On 25 Aug 2009, at 17:28, Douglas N Greve wrote:
> mri_convert segmentation.mgz segmentation
Ah I see,
this raises a question then, of whether the optimizations are still
applicable to WU acquired MP-RAGE data, as we are currently collecting
3T Trio data, and I believe Randy's data is 1.5T Vision data, however
the sequence (our CAP MP-RAGE) is quite similar... can anyone up there
if you send us a volume we'll take a look. Basically Randy's mp-rage had
significantly darker gray matter than we were used to in SPGR and MPRAGE
images. If wm was around 110, I think typical GM is around 75, but Randy's
were around 60.
cheers,
Bruce
On Wed, 26 Aug 2009, Alexander Li Cohen
yes, it was optimized for the mp-rages that Randy B used to collect
there, not for example ADNI.
On Tue, 25 Aug 2009, Michael Harms wrote:
>
> I assume that that flag (-washu_mprage) is somewhat antiquated, right?
> That is, it was included for an older set of scans (generated at WashU
> generate
No, our current "CAP" MPRAGE at WU on the 3T TimTrio is very similar to
the "ADNI" mprage, so that old flag shouldn't be used.
-MH
On Wed, 2009-08-26 at 09:24 -0500, Alexander Li Cohen wrote:
> Ah I see,
> this raises a question then, of whether the optimizations are still
> applicable to WU
Hi,
I'm getting an error trying to run a reconstruction.
I'm working on multnomah and my subjects directory
is: /autofs/space/multnomah_002/users/Cashlab/
I'm using the following command:
[multnomah:Cashlab] (nmr-std-env) recon-all -autorecon1 -autorecon2 -subject
MG25_SurferOutput -i
MG25/MR
Hi, there,
I used FreeSurfer pipeline to study a subject, I convert my .nii file to .mgz
file, and then
send it to FreeSurfer pipeline.Everything works well. Now I want to convert the
wmparc.mgz back to the space that the original volume was.
I tried two command
mri_covert wmparc.mgz -rl orig
We have performed a GLM analysis on pial_lgi surface data between 2
subject groups. We would like to transform the sig.mgh file back from
the average subject surface space to the average subject volume
(brainmask.mgz). It would appear we should use mri_surf2vol, but are
not clear what our v
There's also the flag -mpragewhich can be used, intended for the
mprage developed by Andre van de Kouwe, which I believe is the same as
that now used by Siemens.
Nick
On Wed, 2009-08-26 at 09:37 -0500, Michael Harms wrote:
> No, our current "CAP" MPRAGE at WU on the 3T TimTrio is very simil
Ok, now I'm confused again, because my understanding is that the Andre
van de Kouwe mprage, Siemen's default mprage, and the ADNI mprage really
are not very different in terms of their contrast. Is that not correct?
Assuming they are indeed all similar, are you saying that a modern
"ADNI-like" m
I've just created a new wiki to describe how to do this:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
Guang Zeng wrote:
> Hi, there,
>
> I used FreeSurfer pipeline to study a subject, I convert my .nii file to .mgz
> file, and then
> send it to FreeSurfer pipeline.Everything w
For WM, you can use aparc+aseg.mgz and use indices 2 and 41. Do you want
a particular GM or all GM?
Ed Gronenschild wrote:
> Doug,
>
> The file "segmentation.mgz" doesn't exist.
> I think that you mean that segmentation.mgz stands
> for either WM or GM. Can you provide me the
> exact file names o
yes, that's true. The difference is between the SPGR and the MP-RAGE. If we
don't know which it is we have to try to figure out the contrast and noise
characteristics (spgr has worse contrast and less noise)
On
Wed, 26 Aug 2009, Michael Harms wrote:
>
> Ok, now I'm confused again, because my u
You can use the identity, something like this:
mri_surf2vol --identity subjectname --hemi lh --o vol.lh.thickness.nii
--surfval lh.thickness --template ../mri/orig.mgz
doug
Holly Bridge wrote:
> We have performed a GLM analysis on pial_lgi surface data between 2
> subject groups. We would like
Looks like that is a pretty weak computer. Can you run it on a stronger
computer?
Rodrigo Zepeda wrote:
> Hi,
>
>I'm getting an error trying to run a reconstruction.
>
> I'm working on multnomah and my subjects directory
> is: /autofs/space/multnomah_002/users/Cashlab/
>
> I'm using the foll
Thanks. I tried running it on oct and I'm getting another error earlier on
recon process.
The subjects directory is: /homes/11/rzepeda/Recon
I'm using the following command:
[oct:~/Recon] (nmr-std-env) recon-all -autorecon1 -autorecon2 -subject
MG25_SurferOutput -i
MG25/MRI/1.3.12.2.1107.5.2.30
These are often very hard problems to track down so please send a full
bug report
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
doug
mi...@nmr.mgh.harvard.edu wrote:
> Hello All,
>
> I'm getting an error similar to another some months back.
> http://www.mail-archive.com/freesurfer@nmr.mgh.har
To use --fwhm you have to specify the sign of the contrast (this
implements the gaussian random fields). If a sign is not given in the
wiki, can you fix it?
doug
pkun...@nmr.mgh.harvard.edu wrote:
> Hi all,
>
> I was going through the FSFAST TUTORIAL from wiki(
> https://surfer.nmr.mgh.harvard.
Sorry for the question but what is VentralDC? I mean what means the acronym
--
Enviado do meu celular
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
--- Novo Netfilter 3.2 www.Netfilter.com.br
--- N
I believe the acronym stands for ventral diencephalon.
Jesse
On Wed, Aug 26, 2009 at 8:53 PM, Pedro Paulo de Magalhães Oliveira Junior <
p...@netfilter.com.br> wrote:
> Sorry for the question but what is VentralDC? I mean what means the acronym
>
> --
> Enviado do meu celular
>
> ---
oops "diencephalon" it should have been
On Wed, 26 Aug 2009, Pedro Paulo de
Magalhães Oliveira Junior wrote:
Sorry for the question but what is VentralDC? I mean what means the acronym
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https
ventral diecephalon. It's a mismash of a bunch of different stuff. I
think the CMA pubs have more details on it.
Bruce
On Wed, 26 Aug 2009, Pedro Paulo
de Magalhães Oliveira Junior wrote:
Sorry for the question but what is VentralDC? I mean what means the acronym
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