Hi,
Is it possible to run recon-all so that both control point edits and
brain volumes can be processed with a single command?
Currently I use
recon-all -autorecon2-cp -autorecon3 -subjid
for corrections to control points
and
recon-all -autorecon2-pial -autorecon3 -subjid
for corrections to
I think you are right
I bet you can choose to control FDR locally (clustering?)
2008/8/28 jorge luis <[EMAIL PROTECTED]>
> Dear Glen, there is something you have to take into account when using FDR
> separately at various regions of a parcelled brain. It do not control de
> Global FDR if the nul
Quoting Polina Golland <[EMAIL PROTECTED]>:
http://www.na-mic.org/Wiki/index.php/Mbirn:_Machine_Learning_Tools
If you scroll down to the middle of the page, there is a link to
download the classification scripts.
Polina.
On Thu, Aug 28, 2008 at 04:02:09PM -0400, Bruce Fischl wrote
Before viewing it on the surface, you should view it in the volume with
tkmedit. You can also load the surfaces in the volume (they show up as
lines), and see if the surfaces intersect the activatino. Also, please
remember to provide us with all the relevant info. See
surfer.nmr.mgh.harvard.
Thanks a lot for clarification, Bruce.
Best,
Martin
On Thursday 28 August 2008 22:00:29 Bruce Fischl wrote:
> Hi Martin,
>
> I think "recon-all -autorecon2-cp -autorecon3" should be fine (it's a
> superset of the -wm stuff).
>
> Bruce
>
> On Thu, 28 Aug 2008, Martin Kavec wrote:
> > Greetings to
Hi Sebastian,
I think Polina might have packaged something up for either ITK or mBIRN.
Polina?
Bruce
On Thu, 28 Aug 2008, Sebastian Gluth wrote:
Hi,
I'm planning to analyze cortical thickness data and read about this
classification and permutation approach by Golland et al. (2002) and Golla
Hi Martin,
I think "recon-all -autorecon2-cp -autorecon3" should be fine (it's a
superset of the -wm stuff).
Bruce
On Thu, 28 Aug 2008, Martin Kavec wrote:
Greetings to all,
I have several pathological subjects, which need substantial editing involving
removing of dura reminders, filling W
Hi,
I'm planning to analyze cortical thickness data and read about this
classification and permutation approach by Golland et al. (2002) and Golland &
Fischl (2003) in order to account for multivariate effects.
Is this classification procedure included in FreeSurfer (in form of a tool or a
Matlab
Greetings to all,
I have several pathological subjects, which need substantial editing involving
removing of dura reminders, filling WM due to the lesions, and adding control
points due to the WM atrophy. I ran "recon-all -all" first to have initial
reconstruction, which helps me to focus on co
Silviu,
MC-full is really slow. you can get almost same results using mc-z that is
quicker.
thanks
pratap
> Hello!
>
> I was running the full Monte Carlo simulation on the 40 subjects tutorial
> data (following the Group Analysis tutorial, with mri_glmfit from command
> line) and I see the sim
Hello!
I was running the full Monte Carlo simulation on the 40 subjects tutorial data
(following the Group Analysis tutorial, with mri_glmfit from command line) and
I see the simulation is still running after 10 days...
I was wondering if this was normal or something is wrong. (using a single 2
Dear Glen, there is something you have to take into account when using FDR
separately at various regions of a parcelled brain. It do not control de Global
FDR if the null hypothesis is true in many of these regions.
Although FDR provides strong control of false positives under the null
hypothe
did you change it, or doesn't it match the first time you bring it up? Tk
has this somewhat strange property where you have to hit the return key
for a change to really take effect
On Thu, 28 Aug 2008, Nicola Hobbs wrote:
Hi all,
We've noticed that the min threshold value in the configure ove
Hi all,
We've noticed that the min threshold value in the configure overlay
display toolbar doesn't correpond to the value displayed on the scale
bar. Could someone explain this difference please?
Thanks for your help.
Nicola
--
Nicola Hobbs
Dementia Research Centre
National Hospital for
Hi Hong,
we've just rewritten the longitudinal stream to be significantly more
accurate. Unfortunately (for us) Nick is on vacation at the moment so
you're question will have to wait a few days for an answer. Repost next
week if you haven't heard before then.
Bruce
On Thu, 28 Aug 2008, Xie, H
Hello, group,
I am running longitudinal process step by step following the wiki page of
12 differences between longitudinal and recon-all process. But some needed
files are not generated by these 12 steps, for example, brain.mgz, wm.seg.mgz,
wm.asegedit.mgz, aseg.auto_noCCseg.mgz, wm.mgz
Hello, Group,
I tried to registered the fsl average of one subject .gfeat to his freesurfer
surface. After manual correction of register files, the ROIs of ,gfeat become
much smaller on the freesufer surface (including less cortical areas). please
help me with this problem.
Thank in advance,
Hello, group,
I am running longitudinal process step by step following the wiki page of 12
differences between longitudinal and recon-all process. But some needed files
are not generated by these 12 steps, for example, brain.mgz, wm.seg.mgz,
wm.asegedit.mgz, aseg.auto_noCCseg.mgz, wm.mgz, fi
Dear Manja,
It is statistically valid for the threshold suggested by FDR to vary in
the different hemispheres. The reason is that FDR defines a proportion,
not an absolute. The FDR procedure suggests a p-value threshold with the
property that of all positive results at that threshold, one can expe
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