Hello i am trying to access the data files in 3D but i am having problems
opening the files using the command syntax given on the website.
I have set my own pathway using my own data;
“/projects/pbic1030/Micahel/subjects/Subj1/fsaverage/surf/”
However, one i progress with the code past this poi
rror message you
got.
Thanks,
Ruopeng
On Jun 14, 2017, at 9:26 AM, Michael Davies
mailto:michael.davie...@hotmail.com>> wrote:
Hello i am trying to access the data files in 3D but i am having problems
opening the files using the command syntax given on the website.
I have set my ow
behalf of Ruopeng Wang
Sent: 14 June 2017 15:54:15
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] viewing surfaces in 3D using freeview
You didn't call freeview there... Try adding "freeview -f " at the beginning of
the command.
On 06/14/2017 11:02 AM, Michael D
Sent: 14 June 2017 18:46:00
To: Freesurfer support list
Subject: Re: [Freesurfer] viewing surfaces in 3D using freeview
Hi Michael
can you send us the full command line and screen output of any command
that you ran that fails and you want our help with?
thanks
Bruce
On Wed, 14
Jun 2017, Michael
Hello, i am having problems accessing the 3D surfaces of my data. Is there any
advice you could provide for me please?
bash-4.1$ freeview -f \
> /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0
> \
> /projects/pbic1030/Michael/subjects/
Hello, i am having problems loading the 3D surface for my data. I was wondering
if you could provide any advice please? This is the command code i put into the
terminal;
bash-4.1$ freeview
-f/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visi
ng 3D surfaces
Hi Michael
you need to have FreeSurfer in your path or nothing will work. Have you
sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the
environment?
cheers
Bruce
On Thu, 15 Jun 2017, Michael Davies wrote:
> Hello, i am having problems accessing the 3D su
on behalf of Bruce Fischl
Sent: 15 June 2017 15:19:21
To: Freesurfer support list
Subject: Re: [Freesurfer] viewing 3D surfaces
you are not calling freeview in this command. Try putting freeview at the
start
On Thu, 15 Jun 2017, Michael Davies wrote:
>
> Hi Bruce, i am still getting error me
the '/' in front of "surf".
On 06/15/2017 11:45 AM, Michael Davies wrote:
Hi Bruce, i'm getting closer to opening it now. But the final command
/surf/lh.pial \ didnt work this time. Any further suggestions?
Kind regards, Michael
bash-4.1$ freesurfer_setup_freeview
: [Freesurfer] viewing 3D surfaces
Hi Michael
I think you need to do a Unix tutorial. That path is wrong.
cheers
Bruce
On Thu, 15 Jun
2017, Michael Davies wrote:
>
> Hi Bruce, i'm getting closer to opening it now. But the final command
> /surf/lh.pial \ didnt work this time. Any furth
mmand.
cheers
Bruce
On Thu, 15 Jun 2017, Michael
Davies wrote:
>
> Hello Bruce, how do you mean the path is wrong? I am curious as the data
> loaded just.
>
>
> Kind regards, Michael
>
> ___
Hello, i am currently looking at the WM Volume in heat mode and am curious as
to if i need to fill in all the small missing voxels located within the
boundary as well as the bigger holes?
Kind regards, Michael
___
Freesurfer mailing list
Freesurfer@nm
Hello, i am currently having problems with the code required to regenerate the
surface when editing the WM Volume. I was wondering if you could provide any
tips or advice as to where i am going wrong please?
Kind regards, Michael
bash-4.1$ freesurfer_setup_freeview
freesurfer-Linux-cen
: Re: [Freesurfer] Regenerating the WM Volume surface
can you include your full command line? It looks like you typed:
recon-all -autorecon2-wm -autorecon3 -Subj2
when probably what you wanted was
recon-all -autorecon2-wm -autorecon3 -s Subj2
cheers
Bruce
On Tue, 20
Jun 2017, Michael Davies
Hello, i have been trying to regenerate the surface on one of my subjects but
keep having a problem where the terminal is saying there is a missing file
name. Do you have any suggestions please?
Kind regards, Michael
bash-4.1$ freesurfer_setup_freeview
freesurfer-Linux-centos6_x86_64
Hello, i have been trying to regenerate the surface on one of my subjects but
keep having a problem where the terminal is saying there is a missing file
name. Do you have any suggestions please?
Kind regards, Michael
bash-4.1$ freesurfer_setup_freeview
freesurfer-Linux-centos6_x86_64
g (that is, for the file that you give to recon-all as the input).
>
> cheers
> Bruce
>
>
> On Mon, 3 Jul 2017, Michael Davies wrote:
>
>>
>> Hello, i was wondering if you could possibly help me with a subjects file
>> that has loaded badly. It not only
Hello, I have encountered a lopsided hemisphere when analysing the data. What
procedure do i need to employ to fix the problem? Any advice would be greatly
appreciated!
Kind regards, Michael
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
h
] lopsided hemisphere
Hi Michael
I don't think there is really a problem here - it is just that either the
brain is oriented strangely or it indeed asymmetric. In any case the
segmentations and surfaces look accurate
cheers
Bruce
On Tue, 4 Jul 2017, Michael Davies
wrote:
>
> He
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