Hi Bruce,
Yes I am trying to do some quantitative analysis rather than just displaying
the patches. The only way I know for getting the vertex indices and the
coordinations is reading it into matlab.
(1) flat = read_patch(‘lh.cortex.patch.flat’);
This command worked today! I rebooted my system
Bastian,
Hi, I've posted a new mris_convert which should solve the problem for
you. It's built for Centos 6, so if you need it for another platform,
let me know. It's here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
Nick
On Wed, 2014-05-28 at 11:42 +0200
Daniel found your problem as he mentioned in his previous email (see
below). Change the qdec table to have the name of the subject be
54987500_output.
Also, I noticed that you have gender as a continuous variable. It should
be discrete
Original Message
Subject:
Your subject name is wrong.
You are saying the subject name is: 54987500
While it is actually: 54987500_output
You should either change the name of the SUBJECT directory or change the
subject id you are giving to mri_glmfit.
HTH
D
On Wed, May 28, 2014 at 5:17 PM, Saloni Sharma wrote:
Many thanks! It worked.
On Wed, May 28, 2014 at 4:19 PM, Douglas N Greve
wrote:
> It has to be a text/ascii file
> On 05/28/2014 03:45 PM, Yu(余)Qijing(奇静) wrote:
> > Dear Freesurfers,
> >
> > I am experiencing the following problem when I load the qdec.table.dat
> > file in qdec:
> >
> > Loading
It has to be a text/ascii file
On 05/28/2014 03:45 PM, Yu(余)Qijing(奇静) wrote:
> Dear Freesurfers,
>
> I am experiencing the following problem when I load the qdec.table.dat
> file in qdec:
>
> Loading data table /Volumes/fMRI/Scanner_Data/qdec/qdec.table.dat...
> QdecDataTable::Load: will attempt
Samuel,
Unfortunately the program that's failing is 'mritotal', which is an MNI
tool that is distributed with freesurfer, so it's unlikely that we'll
track this down anytime soon.
However, this program is only run after our primary talairach alignment
utility fails, and it appears from your recon
Saloni,
are you certain that you ran recon-qcache on subject 54987500? the
error message says that the file lh.thickness.fwhm10.fsaverage.mgh is
missing, and this file is created by -qcache. i'd suggest running:
recon-all -s 54987500 -qcache
then confirm that this file exists.
Nick
Dear Freesurfers,
I am experiencing the following problem when I load the qdec.table.dat file
in qdec:
Loading data table /Volumes/fMRI/Scanner_Data/qdec/qdec.table.dat...
QdecDataTable::Load: will attempt to open as Mac text file...
Number of columns: 4
fsid column:1
Number of factors:
please send the command line without variables
On 05/28/2014 02:02 PM, Ben Mooneyham wrote:
> Hi all,
>
> I'm trying to transform a mean functional image into subject (T1)
> space using mri_vol2vol. Originally, my code worked successfully, but
> in attempts to re-run the procedure, both on the
The registration completed fine.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Wednesday, May 28, 2014 11:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dt_recon error
Hi all,
I'm trying to transform a mean functional image into subject (T1) space
using mri_vol2vol. Originally, my code worked successfully, but in
attempts to re-run the procedure, both on the same data and on additional
data, I've encountered an error in which the log reports an "ERROR: Option
u
You will need to install libboost v1.41 onto your system. You should be
able to install it using yum:
$>yum install boost-devel
However, its possible that the version you get thru this method may be
incompatible with the version required by freesurfer. If the above does
not fix your issue, the
use mri_segstats
run it with --help to get docs and examples
doug
On 05/28/2014 01:21 PM, sabin khadka wrote:
> Hi all,
> I want to extract mean cortical thickness, surface area of an ROI I
> created with some clusters that showed some group difference. I
> already have the ROIs I need.
> What
Hi all,
I want to extract mean cortical thickness, surface area of an ROI I created
with some clusters that showed some group difference. I already have the ROIs I
need.
What is the easiest way to extract mean values of ROI from all the subjects?
Thanks,
Sabin
Does anybody know a straightforward way to take a labeled vtk image and
create a freesurfer image with the accompanying annotation file? Or is
there a way to create an annotation file from the list of vertices and
labels?
Ronald Pierson
___
Freesurf
Hi, I had mri_cvs_register die on me when it couldn't find a shared
library. Relevant bit is (full log is attached):
mris_resample: error while loading shared libraries:
libboost_program_options.so.5: cannot open shared object file: No such file
or directory
Freesurfer bugr info:
---
Hi Martin,
Thanks for your response. When I run the command alone, the following
message appears:
mri_convert --frame 0 ./tmp-0001_base_lh_thickness_U5R6w6/glm/beta.mgh
./tmp-0001_base_lh_thickness_U5R6w6/beta0.mgh
bash: /Applications/freesurfer//bin/mri_convert: cannot execute binary file
I'v
and the registration?
On 05/28/2014 08:46 AM, Weber, Wade (weberw) wrote:
> Hi Doug,
>
> It ran completely through to the end, but when I open up and inspect the data
> there is nothing there except for a few white/grey voxels.
>
> Wade
>
> -Original Message-
> From: freesurfer-boun...@nmr
Hi Doug,
It ran completely through to the end, but when I open up and inspect the data
there is nothing there except for a few white/grey voxels.
Wade
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
Hi Alessia
if the talairach is really incorrect that can mess things up. I suspect
it's not just the CC, but the aseg as a whole that doesn't look good since
we do use the talairach.xfm for some initializations if it is present.
cheers
Bruce
On Wed, 28
May 2014, Alessia Giuliano wrote:
Dear Freesurfer-Experts,
I would like to create gifti-surfaces to use in matlab.
That's what I am doing so far (latest FS-Version):
mris_convert lh.white lh.white.gii
I then try to open it using the "gifti" command (g=gifti('file.gii'))
(http://www.artefact.tk/software/matlab/gifti/)
however,
Dear FreeSurfer team,
in order to verify that the segmentation of Corpus Callosum was independent
from the initial orientation of the subject MR scan I repeated the recon-all of
FreeSurfer in two conditions:
1- when the initial alignement of the scan to the MNI space was gross;2- when
the initi
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