hi Jose,
why don't you use MNE for this? MNE is designed to work smoothly with
FreeSurfer.
http://martinos.org/mne/
Cheers,
Alex
On Thu, Apr 25, 2013 at 7:35 PM, José Ángel Pineda
wrote:
> Dear expert,
>
> I am doing source reconstruction with MEG.
>
> First, I am corregistering my head surfac
hi,
when trying to read the following .annot file:
https://dl.dropboxusercontent.com/u/2140486/annot_pb/left_mc-z.negative.sig.ocn.annot
using the following matlab code:
--
[vertices, label, colortable] =
read_annotation('left_mc-z.negative.sig.ocn.annot');
unique(label)
unique(colortable.table
vector has a structureID value.
Why do I get 0 in label if 0 is not in colortable.table(:, end)?
thanks
Alex
On Mon, Aug 26, 2013 at 10:06 PM, Douglas N Greve
wrote:
> Hi Alex, have you looked at the read_annotation help?
> doug
>
>
>
>
> On 08/26/2013 03:37 PM, Alexandre
ring name.
>
> PRECONDITIONS
>
> o must be a valid FreeSurfer annotation file.
>
> POSTCONDITIONS
>
> o will be an empty struct if not embedded in a
> FreeSurfer annotation file.
>
>
> On 08/26/2013 05:35 PM, Alexandre Gramfort wrote:
>&g
the label array.
thanks
Alex
On Tue, Aug 27, 2013 at 6:32 PM, Douglas N Greve
wrote:
>
> I think the 0s represent "unknown" areas. In this case, vertices that were
> not part of any cluster. Does that make sense?
> doug
>
>
>
>
> On 08/27/2013 07:47 AM, Alex
> For aparc, that is the corpus callosum. It just means that it was in the
> color table when the annotation file was created. It is not necessary
> that it be in the annotation itself. Can you ignore it?
now that I have your approval to ignore it yes :)
thanks all clear.
Alex
__
Hi,
after running recon-all on many datasets without any manual
intervention, it looks like I finally have to.
As you can see in :
https://dl.dropboxusercontent.com/u/2140486/Screen%20Shot%202013-08-28%20at%2013.16.52.png
the CSF is segmented as gray matter while white+gray matters are merged.
hi,
what we do with MEG in the MNE package is indeed store downsampled
overlays (that actually have a temporal dimension). More specifically we
store the values e.g. only at the vertices of the ico5 subdivision and
store the ico 5 vertex indices and overlay values. Then to display them
on the high
using the mris_expand from that
> version on the recon-all results from a 5.1.0 segmentation to see if the
> issue truly is the expand binary or not.
>
> Any other suggestions you all have would be appreciated.
>
> Thanks,
> Andrew
>
Dear Ruopeng,
to reproduce the problem with :
MatrixMultiply: m2 is null! and the seg fault.
$source /usr/local/freesurfer/nmr-stable51-env
$cd ~gramfort/cluster/work/data/MNE-sample-data/subjects
$setenv SUBJECTS_DIR $PWD
$freeview -f sample/surf/lh.inflated
if you cannot access this folder yo
> Alex, since you're in the Martinos center, can you try source the dev
> version just to see if the same problem exists?
I just tried after sourcing /usr/local/freesurfer/nmr-dev-env
and got the same segfault with MatrixMultiply: m2 is null!
I tried on the machine: megmix
Alex
Hi Kathy,
subprocess.check_output
was introduced in python 2.7. You use 2.6
I recommend to upgrade if possible.
Otherwise we need to fix this
Alex
On Fri, May 4, 2012 at 3:44 PM, keepmoon wrote:
> Dear Michael,
>
> I try to install Python and Pysurfer following the instructions
> (using easy
hi,
this problem has been reported and fixed.
You should install the latest hot fit with:
https://github.com/nipy/PySurfer/zipball/master
then do from the folder:
python setup.py install
HTH
Alex
On Sat, May 5, 2012 at 10:09 PM, keepmoon wrote:
> Hi Michael and Alex,
>
> Thanks for your su
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