so you run recon-all, convert to gifti and display that and it doesn't
match the original surface?
On Sun, 8 Sep 2013, Shani Ben Amitay wrote:
Im looking at the gifti and fs surfaces in freeview they are not
aligned.this surface was reconstructed with noaparc and noaseg.maybe
transformation file is missing?
thank you
shani
בתאריך 8 בספט 2013 16:59, מאת "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>:
Hi Shani
how do you know it is shifted?
Bruce
On Sun, 8 Sep 2013, Shani Ben Amitay wrote:
Sorry to bug again with this issue when converting
the freesurfer surface to
GIFTI using mris_convert the surface is shifted in
space.
Does anyone know how to transform it to freesurfer
space?
Thanks!
Shani
On Tue, Sep 3, 2013 at 12:34 PM, Saad Jbabdi
<s...@fmrib.ox.ac.uk> wrote:
You need to convert your surface file into a
format that
workbench understand (GIFTI):
mris_convert lh.whiteinraw lh.whiteinraw.surf.gii
Cheers
Saad
On 3 Sep 2013, at 10:57, Shani Ben Amitay
<shani.hol...@gmail.com>
wrote:
Thank you!Still somehow I haven't manage to
make it work
when I ran the suggested command I get an
error saying :
ERROR, Command Failed: Parse Error while reading
lh.whiteinraw:
error occurred while parsing element line number: 1
column
number: 1.
Any advise?
Thanks again
Shani
On Mon, Sep 2, 2013 at 10:18 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
thanks Matt
Bruce
On Mon, 2 Sep 2013, Glasser, Matthew wrote:
> Hi Bruce,
>
> Connectome Workbench commandline utilities
can do
this with FSL warp
> fields:
>
> wb_command -surface-apply-warpfield
>
> One needs to use the inverse warp as the
<warpfield> argument and the
> forward warp as the -fnirt <forward-warp>.
>
> Peace,
>
> Matt.
>
> On 9/2/13 11:19 AM, "Bruce Fischl"
<fis...@nmr.mgh.harvard.edu> wrote:
>
>> A veritable game of telephone! Thanks
Jesper.
Matt?
>>
>> On Mon, 2 Sep 2013, Jesper Andersson wrote:
>>
>>> Hi guys,
>>> I didn't think we had any tools for doing
that,
and said so much on the
>>> FSL
>>> mailbase. But apparently the WashU people
has
something that does just
>>> that
>>> for you. I think the best person to
contact
about the details is Matt
>>> Glasser.
>>>
>>> J
>>>
>>> On 2 Sep 2013, at 15:58, Saad Jbabdi
<s...@fmrib.ox.ac.uk>
>>> wrote:
>>>
>>> Hi In Probtrackx, this is done
internally.
>>> If you just want to transform the vertex
coordinates, then I think
>>> you'll need to play with the FNIRT source
code -
I've CC'd Jesper who
>>> knows better.
>>>
>>> Cheers,
>>> Saad
>>>
>>>
>>>
>>> On 2 Sep 2013, at 15:56, Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>
>>> you might check on the FSL list. I
think
I've seen some
>>> traffic indicating that there are
some
tools for doing
>>> this. I'l cc Saad as he might know
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Mon, 2 Sep 2013, Douglas Greve
wrote:
>>>
>>> Hi Shani, I don't think you
can
apply a FNIRT
>>> transform to a surface.
>>> doug
>>> On 9/2/13 8:20 AM, Shani Ben
Amitay
wrote:
>>> Dear freesurfer people,
>>> Any idea whether I can apply
transformation
>>> that was calculated by fsl
>>> fnirt on the white/pial
surfaces
calculated
>>> using the freesurfer
>>> stream?
>>> Thanks!
>>> Shani
>>>
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>>> University of Oxford, FMRIB Centre
>>>
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>
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University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
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