Hi Shani,then what? How do you convert to gifti? And does that surface look differently before and after conversion in freeview?
BruceOn Sun, 8 Sep 2013, Shani Ben Amitay wrote:
'm running the following commands to reconstruct the white and pial
surfaces(non-human data)
mri_pretess mri/filled/filled.mgz 255 mri/brain.mgz mri/filled-pretess255.m
gz
mri_tessellate mri/filled-pretess255.mgz 255 surf/lh.orig.nofix
mris_extract_main_component surf/lh.orig.nofix surf/lh.orig.nofix
mris_smooth -nw surf/lh.orig.nofix surf/lh.smoothwm.nofix
mris_inflate -no-save-sulc surf/lh.smoothwm.nofix surf/lh.inflated.nofix
mris_make_surfaces -noaparc -noaseg -mgz -T1 brain rat1 lh -pial
Thank you
Shani
[cleardot.gif]
On Sun, Sep 8, 2013 at 6:37 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
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
>>>
_______________________________________________
>>> Freesurfer mailing
list
>>>
Freesurfer@nmr.mgh.harvard.edu
>>>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>> The information in this
e-mail is
intended
only for the
>>> person to whom it is
>>> addressed. If you
believe this
e-mail was
sent to you in
>>> error and the e-mail
>>> contains patient
information, please
contact the Partners
>>> Compliance HelpLine at
>>>
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If the e-mail was
>>> sent to you in error
>>> but does not contain
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information,
please contact
>>> the sender and properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>>> --
>>> Saad Jbabdi
>>> 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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--
Saad Jbabdi
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
