; On 02/23/2016 10:17 AM, Maheen Siddiqui wrote:
> > I changed the directory and it ran, but with errors. I had to change
> > the last part --surf lh.seghead --surf-smooth 10 because it does not
> > recognise --surf. When I change this to --o, it runs but with errors.
> >
&g
I still get the error option --surf unkown
On Mon, Feb 29, 2016 at 7:52 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
>
> try this version
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize
>
>
> On 02/23/2016 10:17 AM, Maheen Siddi
Can't locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup
module)
Maybe there was a step missed of the installation? If everything is installed
properly then recon-all works perfectly. Maybe make sure everything that was
required from installation has been done. Or try it
Thanks very much, I'll have a look!
On Fri, Feb 26, 2016 at 4:13 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
> yes, they are documented pretty extensively on our wiki
> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
>
> On Fri, 26 Feb 2016, Maheen Sidd
wrote:
> Maheen,
>
> it sounds like a question that could be better answered by the Homer2 list.
>
> hth
> d
>
> On Fri, Feb 26, 2016 at 8:13 AM, Maheen Siddiqui
> <maheen.siddiqu...@gmail.com> wrote:
> > Dear FreeSurfer Users,
> >
> > I have a
16777213 means it's a quad file, not a triangle file. I still
> would have thought we could read it fine. Do you want to email us the
> surface file and someone will take a look?
>
>
> On Tue, 23 Feb 2016, Douglas Greve wrote:
>
> Can you load it in tksurfer or freeview?
&g
wrote:
>
>
> On 2/23/16 9:39 AM, Maheen Siddiqui wrote:
>
> It seems to be giving me an error and saying it cannot read the
> seghead.mgz file.
>
> Is it in the same directory where you are running the command? If so, what
> is the terminal output?
>
>
> From my
ze --i seghead.mgz --min 0.5 --surf lh.seghead --surf-smooth 10
>
>
>
>
> On 2/23/16 9:22 AM, Maheen Siddiqui wrote:
>
> Is it possible to use a different function? Can I use mri_vol2surf on the
> seghead.mgz file? Or do you think that mkheadsurf is the right one to be
> usin
freeview?
>
>
> On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
>
> Hi FreeSurfer users,
>
> I have used the "mkheadsurf" command to create a head surface for my
> subject. However when I try to use "read_surf" to read the "lh.seghead"
> file that is c
Hi,
Yes I can load it in freeview.
On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> Can you load it in tksurfer or freeview?
>
>
> On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
>
> Hi FreeSurfer users,
>
> I have used the "m
Hi FreeSurfer users,
I have used the "mkheadsurf" command to create a head surface for my
subject. However when I try to use "read_surf" to read the "lh.seghead"
file that is created, the magic number is not one that is recognised.
Having read some previous posts/questions with similar
Dear FreeSurfer users,
I have used the "mkheadsurf" function to create "lh.seghead" in the surf
folder of my subject. Now I am trying to extract the vertices and faces of
"lh.seghead" in the following way:
*[vertex_coords, faces] = read_surf('lh.seghead')*
but get an error in
Dear FreeSurfer Users,
I have a T1 weighted MRI scan and have run the recon-all command on it. For
my steps moving forward I need to have 4 layers of tissue i.e. 4
segmentation files - GM, WM, CSF and extra cerebral tissue. Which of the
outputs from recon-all will give me the segmentation? I
to import the surfaces I have
>> into Homer2 Atlas Viewer and for this I need whole surface/volume files
>> rather than the individual hemispheres. Does anybody have experience
>> combining the hemispheres?
>>
>>
>> Many thanks,
>>
>>
>>
experience combining the
hemispheres?
Many thanks,
Maheen
Maheen Siddiqui
BBSRC LIDo PhD Student
Centre for Brain and Cognitive Development
Birkbeck, University of London
London
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