[Freesurfer] recon-all issue (CSF seg as gray matter)

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.

Re: [Freesurfer] pb reading .annot in matlab/python

in a FreeSurfer annotation file. On 08/26/2013 05:35 PM, Alexandre Gramfort wrote: hi doug, I thought so. Did I miss something obvious? My version is: % read_annotation.m % Original Author: Bruce Fischl % CVS Revision Info: %$Author: nicks $ %$Date: 2011/03/02 00:04:12 $ %$Revision

Re: [Freesurfer] pb reading .annot in matlab/python

. thanks Alex On Tue, Aug 27, 2013 at 6:32 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu 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, Alexandre Gramfort wrote: hi Doug, I am

Re: [Freesurfer] pb reading .annot in matlab/python

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

[Freesurfer] pb reading .annot in matlab/python

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)

Re: [Freesurfer] pb reading .annot in matlab/python

of the label 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 gr...@nmr.mgh.harvard.edu wrote: Hi Alex, have you looked at the read_annotation help? doug On 08/26/2013 03:37 PM, Alexandre

Re: [Freesurfer] Downsampling/decimating overlays (not surfaces)

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

Re: [Freesurfer] load multiple overlays with different colors

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 keepmoon1...@googlemail.com wrote: Hi Michael and

Re: [Freesurfer] load multiple overlays with different colors

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 keepmoon1...@googlemail.com wrote: Dear Michael, I try to install Python and Pysurfer following the

Re: [Freesurfer] Freeview chrash

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

Re: [Freesurfer] Freeview chrash

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

Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 98, Issue 29

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 From: Alexandre Gramfort [gramf...@nmr.mgh.harvard.edu] Sent: Tuesday