Re: [Freesurfer] FreeSurfer transforms

[Vinny K]

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Hi Bruce,

I'm looking at diencephalic and midbrain structures and their various
subdivisions for application to tractography.  I used the thalamic nuclei
segmentation feature in the development version of FreeSurfer to obtain
labeling of individual thalamic nuclei that is run in addition to aseg,
which has worked out great.  However, for other deep brain structures such
as the subthalamic or pontine nuclei (e.g. pedunculopontine), to my
knowledge, aseg does not parcellate these out; however, they are available
MNI space.  FreeSurfer gives an excellent registration of labeled atlas
structures in patients with big ventricles, which I've had difficulty with
using other registration tools.  I was wondering if there was a way that I
could bring some of these labeled nuclei in MNI space into the patient's T1
space using FreeSurfer.

Thanks,

Vinny

On Sat, Oct 19, 2019 at 12:16 PM Bruce Fischl 
wrote:

> Hi Vinny
>
> why do you need to brain structures from MNI space? Isn't the aseg
> sufficient? Or are there structures that are not in the aseg?
>
> cheers
> Bruce
> On Sat, 19 Oct
> 2019, Vinny K wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi,
> > FreeSurfer does a great job in registering atlas structures to patients
> with
> > big ventricles.  I'd like to use the calculated FreeSurfer transforms in
> > bringing additional subcortical structures from MNI space (either MNI305
> or
> > MNI2009b) into native T1 space.  Can you please advise on how to do this?
> >
> > Thanks,
> >
> > Vinny
> >
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Re: [Freesurfer] ECC or non-ECC Memory?

[Sotiris Michos]

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Dear all,

This is just to close up this question. After some correspondence with the
lab's members, I was informed that due to the imaging nature of the
software ECC is not "needed" but advisable. The lab's computers are all
equipped with ECC memory. However, a double run of an analysis is deemed
adequate to over come the rare case of any such errors, even when non-ECC
is used.

I would like to thank everyone who contributed to this questions with their
comments as well as the lab's members that assisted me with this issue.

Best Regards,
Sotiris Michos
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Re: [Freesurfer] FreeSurfer transforms

[Bruce Fischl]

Hi Vinny

why do you need to brain structures from MNI space? Isn't the aseg 
sufficient? Or are there structures that are not in the aseg?


cheers
Bruce
On Sat, 19 Oct 
2019, Vinny K wrote:




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Hi,
FreeSurfer does a great job in registering atlas structures to patients with
big ventricles.  I'd like to use the calculated FreeSurfer transforms in
bringing additional subcortical structures from MNI space (either MNI305 or
MNI2009b) into native T1 space.  Can you please advise on how to do this?

Thanks,

Vinny  

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Re: [Freesurfer] help

[Bruce Fischl]

Hi Asim

can you give us a bit more information? Where does the brainmask come 
from? I believe we should detect the fact that the brainmask.mgz is 
different than the automatically created one (brainmask.auto.mgz) and use 
it instead. Note that the recon editing mode in freeview sets erased voxels 
to "1" instead of "0" so we can keep track of edits. You might want to do 
something similar in whatever stream you are using.


cheers
Bruce



On Fri, 18 Oct 2019, Asim Hassan wrote:



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​Good afternoon,


Is there any other way to incorporate a manually edited brain mask into the
recon all process other than through the recon-mode in freeview?

Thanks!
Asim Hassan
Research Technician II
Waugh Lab
Division of Pediatric Neurology
University of Texas Southwestern Medical Center
Phone: 214-645-9259



UT Southwestern

Medical Center

The future of medicine, today.


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Re: [Freesurfer] FreeSurfer transforms

[Vinny K]

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Hi,

FreeSurfer does a great job in registering atlas structures to patients
with big ventricles.  I'd like to use the calculated FreeSurfer transforms
in bringing additional subcortical structures from MNI space (either MNI305
or MNI2009b) into native T1 space.  Can you please advise on how to do this?

Thanks,

Vinny
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Re: [Freesurfer] can´t open an image in Freeview

[Adam Rytina]

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Hello,

I run the command "$ ldd `which freeview` | grep not" and the result is "not a 
dynamic executable". Do you know where the problem is?

What I read there could be the problem regarding 32bit or 64bit system I´m 
working on. I am running on Windows 10 64bit, 64 bit CPU, 64bit Ubuntu 16.04. I 
downloaded the 6.0.0. Freesurfer version from the official 
page:https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

Please, could you help me?

Thanks a lot
Adam


Od: fsbuild 
Odesláno: pátek 18. října 2019 22:05
Komu: freesurfer@nmr.mgh.harvard.edu 
Kopie: adam.ryt...@outlook.cz 
Předmět: Re: [Freesurfer] can´t open an image in Freeview

Hello Adam,

See if you can run the following command, and if it reports anything is not 
found (you can cut and paste the command)

- R.

$ ldd `which freeview` | grep not

Adam Rytina
October 18, 2019 at 14:31

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Hello all,

I´m new to Freesurfer and I´m struggling with loading an image in FreeView. I 
am running the Freesurfer 6.0.0. on Ubuntu 16.04. Virtual Machine. While 
opening FreeView (typing "freeview" in the shell) just some empty grey windows 
will pop out (please see attached the screenshot). Besides this, everything is 
OK, I successfully tested Freesurfer installation. I haven´t found any simmilar 
issue on the Internet. Thus, please, could you help me to address this issue?

Thanks a lot
Adam

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