i havent used mnc2nii. you can use mri_convert:
mri_convert filename.mnc filename.nii
(or filename.nii.gz to gzip it)
n.
On Tue, 2011-01-25 at 21:51 -0500, Alexander Zaitsev wrote:
> Hello:
> When I am trying to convert mnc file into nifti, the mnc2nii converter
> gives me an error
> $FREESUR
Hello:
When I am trying to convert mnc file into nifti, the mnc2nii converter
gives me an error
$FREESURFER_HOME/mni/bin/mnc2nii fileName.mnc fileName.nii
"Can't find input file fileName.mnc"
Prepending a whole path to the file name does not help - same error message
I am using FreeSurver 5.0.0
the recon-all.log indicates that the build stamp is:
freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20100808
which appears to be an internal release candidate version of stable5, so
its very likely that mri_ca_normalize was rebuilt with an different
utils lib prior to the stable-pub-v5.0.0 release
Hi everyone,
I'm wondering whether there are multiple versions of recon-all v 1.313.2.6
(2010/08/04 15:50:56), and/or mri_ca_normalize stable5.
I have been testing recon-all and compared our output against the sample
processed-data in FS/TUtorial. I found that the output obtained was different
It should not. I've already made the change to our code base. You can
just delete that spec in your version of the script if you want. Thanks
for the note!
doug
Michael Waskom wrote:
> Hi Doug,
>
> This reminds me: in the dt_recon script, when bbregister is used, the
> gradient descent tolera
Hi Doug,
This reminds me: in the dt_recon script, when bbregister is used, the
gradient descent tolerance is changed (the command line includes --tol1d
1e-3 ).
I was just wondering why this happens.
Thanks!
Mike
On Tue, Jan 25, 2011 at 1:31 PM, Douglas N Greve
wrote:
> I get a file-not-found t
Hi:
I am currently configuring Freesurfer 5 in a new workstation that we
received... That workstation has Ubuntu 10.10, and a NVIDIA Quadro FX
1800 graphics card... Could you please send me the detailed steps
necessary to install and configure CUDA support ?...
Sincerely,
--
Gonzalo R
I get a file-not-found to that link, so I can't check it out. But, yes,
you should just be able to use bbregister passing it the low-b as the
template (or whatever you used at the target for motion correction). and
specifying --bold or --t2.
doug
Lena Palaniyappan wrote:
> Dear Doug & others
Dear Doug & others
The FSL page on fa to freesurfer registration (
http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html) contain info that uses
tkregister2.
To determine freesurfer_to_fa space registration file, do we need to go through
the freesurfer_to_struc and then struc_to_fa rooutine g
then the ?h.white is probably the way to go
On Tue, 25 Jan 2011, Gabriele
Arnulfo wrote:
> The electrodes are quite long they're length vary from 10cm up to 15cm
> depends on the subject. they usually have been implanted quite deep in the
> brain.
>
> cheers,
>
> g.
>
> 2011/1/25 Bruce Fischl
>
The electrodes are quite long they're length vary from 10cm up to 15cm
depends on the subject. they usually have been implanted quite deep in the
brain.
cheers,
g.
2011/1/25 Bruce Fischl
> Hi Gabriele
>
> inflated is definitely wrong as it has no meaning in the MRI coords. Any
> idea how deep
Hi Gabriele
inflated is definitely wrong as it has no meaning in the MRI coords. Any
idea how deep the electrodes are? The white might be best as it will
minimize the chances of erroneously assigning the electrode to the wrong
bank of a sulcus.
cheers
Bruce
On Tue,
25 Jan 2011, Gabriele Arn
In our last imaging genetic study (Cerasa et al., Dysbindin C-A-T haplotype is
associated with
thicker medial orbitofrontal cortex in healthy population. Neuroimage 2011 in
press) we showed
similar findings between Freesurfer and VBM analyses.
- Original Message -
From: Douglas N Greve
T
Hi Bruce,
I've a list of intra cerebral electrodes channel position segmented out from
the MRI scans. I would like to convert the computed positions from the MRI
scanner space to freesurfer vertexes. I've already transformed the
coordinates of each point from indexes to Cartesian Space values (in
Try looking at Voets, et al, 2008, in Neuroimage vol 43, pg 665-675.
doug
Ritobrato Datta wrote:
> Hello All,
>
> Are there any papers comparing freesurfer to VBM ?
>
> Can anyone point me to them ?
>
> Thanks
>
> Ri
> ___
> Freesurfer mailing list
> Fr
Hi Christian,
I'm sure it's possible, but you might want to check with the brainvoyager
people, unless someone on the list knows what their coordinate
conventions are
cheers
Bruce
On Tue, 25 Jan 2011, Oertel, Viola wrote:
Dear Freesurfer-user,
I have a general question: if I created a activ
Dear Freesurfer-user,
I have a general question: if I created a activation mask during a fMRI task
with Brainvoyager software, which works with talairach space. Is it possible,
and do you know how, to transform the Talairach space mask into the Freesurfer
analysis?
Thanks,
Christian
Dr. Vi
Hi,
I can send you our latest development build if you want to give it a
try. Please let me know what system you are running freesurfer on.
Best,
Ruopeng
On 1/25/11 9:05 AM, Ruopeng Wang wrote:
> Hi,
>
> The current freeview release does not have that option. However, we've
> added the option in
Hi Gabriele,
what are you trying to accomplish? The "right choice" depends on your
goals.
cheers
Bruce
On Tue, 25 Jan 2011, Gabriele Arnulfo wrote:
> Hi again,
>
> looking in previous emails in the list i found that the best way to find the
> nearest vertex number to a certain point is by using
Hi,
The current freeview release does not have that option. However, we've
added the option in our development code. It should be available soon.
Ruopeng
On 1/25/11 3:47 AM, t...@ms36.hinet.net wrote:
>
> Dear Freesurfer experts,
>
> I use freeview to display the cortical thickness. Is it possib
Hi again,
looking in previous emails in the list i found that the best way to find the
nearest vertex number to a certain point is by using the matlab script
mesh_vertex_nearest. So far I've used it with input parameters: the vertices
read through read_surf(rh_pial) and a matrix of Cartesian Coord
Hi Ritobrato,
We have one that may too interest you:
Winkler AM, Kochunov P, Blangero J, Almasy L, Zilles K, Fox PT,
Duggirala R, Glahn DC. Cortical thickness or grey matter volume? The
importance of selecting the phenotype for imaging genetics studies.
Neuroimage. 2010 Nov 15;53(3):1135-46.
h
Dear Freesurfer experts,
I use freeview to display the cortical thickness. Is it possible to change the color map in color scale bar ? how to make the color map such as use jet color ?
thanks in advance
JLH--- 本郵件來自HiNet WebMail ---___
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