That seems to have worked!
Thanks a bunch!
Best,
Omar
>
> On 08/29/2013 02:54 PM, Omar Singleton wrote:
>> Dear List,
>>
>> I have a couple questions I need help with.
>>
>> First, I am trying to constrain my subcortical (mni305) analysis with
>> mri_glmfit to a certain ROI. Can I run mri_glmfit
I had a similar error when using CentOS on VirtualBox. The error came from
an error in the OpenCL driver.
Are you running a virtualmachine?
If not i would advise trying a different graphics driver.
As to the CentOS/Ubuntu choice. I would go with CentOS as it seems more
stable/constant and is more e
exactly
On Thu, 29 Aug 2013, David Romano wrote:
Hi Bruce,
Just to make sure I understand: When you say "the subject's ?h.sphere.reg
file contains the list of locations on the sphere of each subject", does
that mean that the subject's sphere is a sphere centered at the origin (and
of fixed rad
Hi Bruce,
Just to make sure I understand: When you say "the subject's ?h.sphere.reg
file contains the list of locations on the sphere of each subject", does
that mean that the subject's sphere is a sphere centered at the origin (and
of fixed radius for all subjects), and that the coordinate tripl
Thank you very much Bruce,
I have used mris_anatomical_stats and it worked beautifully.
Cheers
Jesus
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thursday, August 29, 2013 1:19 PM
To: Gomar, Jesus
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [F
Hi Franz, I just programmed a fix into mri_surf2surf. What platform do
you use?
As for the shift, you would not expect them to line up. In fact, that
command line does not make a lot of sense. What it is doing is mapping
the xyz coordinates in the native space to a new tesselation. The xyz
co
On 08/29/2013 02:54 PM, Omar Singleton wrote:
> Dear List,
>
> I have a couple questions I need help with.
>
> First, I am trying to constrain my subcortical (mni305) analysis with
> mri_glmfit to a certain ROI. Can I run mri_glmfit with the --mask flag and
> use a volume mask to constrain it to t
Dear List,
I have a couple questions I need help with.
First, I am trying to constrain my subcortical (mni305) analysis with
mri_glmfit to a certain ROI. Can I run mri_glmfit with the --mask flag and
use a volume mask to constrain it to this space?
Second, if so, then how do I create a mask from
What is your command line? Try it on a single subject to see if it fails
doug
On 08/29/2013 02:00 PM, Pietro De Rossi wrote:
> Hi Doug,
>
> It doesn't seem it is failing on a particular subject...or I am not able to
> get it from the error. Futhermore, nothing changes if I use the --skip flag.
Hi Doug,
It doesn't seem it is failing on a particular subject...or I am not able to get
it from the error. Futhermore, nothing changes if I use the --skip flag.
What does it mean when it says:
"List index out of range"?
Inviato da iPhone
Il giorno 29/ago/2013, alle ore 19:38, Douglas N Greve
Is it failing on one particular subject?
On 08/29/2013 09:38 AM, pietro de rossi wrote:
> Dear FreeSurfers,
>
> I am extracting thickness values through the aparcstats2table command
> line.
>
> Everything works just fine for --hemi lh using the --skip flag.
>
> However, when it comes to the rig
Hi Jesus
I'm not sure if it is computed by default, but you can use
mris_anatomical_stats with the -l option to compute it.
cheers
Bruce
On Thu,
29 Aug 2013, Gomar, Jesus wrote:
Dear all,
I am interested on getting thickness measures of the perirhinal cortex.
I am using version 5.3 and
Hi David
the subject's ?h.sphere.reg file contains the list of locations on the
sphere of each subject. Mapping to another subject would involve looking
up the closest set of vertices on the target subject for each source
subject vertex. mri_surf2surf can do this I believe.
cheers
Bruce
On T
Hi Ian
use
set sdir=$SUBJECTS_DIR/$subject/surf
mris_expand -thickness $sdir/lh.white .5 $sdir/lh.graymid
cheers
Bruce
On Thu, 29 Aug
2013, Ian Charest wrote:
Dear Freesurfers,
I need to generate a surface which lies halfway between the wm/gm border and
the pial
surface so that I can then
Dear all,
I am interested on getting thickness measures of the perirhinal cortex.
I am using version 5.3 and I am aware that a label for the perirhinal cortex
has been created in version 5.2.
However, when I run recon-all I don't get thickness measures of the perirhinal
cortex (just as I do for
Hi everyone,
I'm new to FreeSurfer (so sorry in advance for any failures to make
sense!), and have read through Bruce Fischl's '99 papers on how FreeSurfer
maps the yellow (white?) surface onto a template sphere (equipped with
convexity information), and have tried to go through the introductory
m
Dear FreeSurfers,
I am extracting thickness values through the aparcstats2table command line.
Everything works just fine for --hemi lh using the --skip flag.
However, when it comes to the right hemisphere I get
SUBJECTS_DIR : /usr/local/freesurfer/subjects
Parsing the .stats files
Traceback (m
Dear Freesurfers,
sorry for the bump, but my message seems to have gone unnoticed.
Thanks so much for any ideas.
Franz
Am 22.08.2013 um 13:37 schrieb Franz Liem:
> Dear Freesurfers,
>
> I tried to map a single subject surface to fsaverageX (for the sake of
> demonstration lets take fsaverage6)
Dear Freesurfers,
I need to generate a surface which lies halfway between the wm/gm border and
the pial
surface so that I can then import it in matlab using read_surf.m to get the
vertex coordinates and faces for the surface that, as I said, would not be the
pial surface, but defined at half co
Hi ,
I am new to longitudinal processing using freesurfer. I am about to process
a big dataset
of longitudinal images.
If in the end, I am only interested in norm.mgz file, is there a way I can
speed up the processing time of the entire pipeline?
Since norm.mgz gets created in cross sectional pr
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