Thanks you for your quick answer Doug,Just one clarification, in the correction for multiple comparisons, which is the main difference between the mc-z and the permutation test? rather than making simultaions or working on original data. And Why is 5000 runs recommended to mc-z and 1 for permut
Dear Freesurfer Ninjas,
I have been playing around with the new beta version, and am very
interested in the -FLAIRpial option. I have been using this successfully on
cross-sectional runs, but would like to extend it to cross sectional runs.
I have played around with trying to get this to work, in
Hi Jon
I'm not sure what this means, but -make all is the thing to do in this
case.
cheers
Bruce
On Wed, 6 Feb 2013, Jonathan Holt wrote:
> Just had a cluster of computers lock up, unfortunately resulting in several
> freesurfer jobs terminating prior to completion. It's possible I may have
Hi,
I've been trying to email out for help to the FreeSurfer community, using
the below addresses. However, I am not receiving my own email back, though
I am a member of the mailing list via this email address. Can you tell me
what I'm doing wrong?
Thank you!
Susan Kuo
-- Forwarded mess
Hi Charles,
the FLAIRpial is a recent addition and has only been added to the cross
sectional stream so far. I can take a look at porting this to the longitudinal
stream but probably not for 5.2.
Best, Martin
On Feb 7, 2013, at 7:23 AM, Charles Malpas
wrote:
> Dear Freesurfer Ninjas,
>
> I
Dear freesurfer experts,
I have a question regarding white matter hyperintensities (ie values above
110)..if these are included in the brainmask accurately, ie as white matter
when it is indeed white matter, does hyperintensities still cause problems,
and if so why?
Regards Linn
_
Hi Linn
no, they shouldn't I don't think
cheers
Bruce
On Thu, 7 Feb 2013, Linn Mittlestein wrote:
> Dear freesurfer experts,
>
> I have a question regarding white matter hyperintensities (ie values above
> 110)..if these are included
> in the brainmask accurately, ie as white matter when it is
mc-z is a simulation that replaces the data with smoothed gaussian
noise. permutation uses your data and changes the order of the rows in
the design matrix. If the noise in your data set is Gaussian, they will
give the same result (in theory:). If the noise is not gaussian, then
the mc-z will
Hi FreeSurfer community,
I would like to run '-bedp' with TRACULA, to run the bedpostx option. I
see from the *./subjID/scripts/trac-all.cmd* file that the actual command
issued was *bedpostx_seychelles*, which allows for the PBS queueing system
running on seychelles and is used by the Martinos
On 02/04/2013 02:10 AM, Sean Hatton wrote:
> Hi FreeSurfers,
>
> These should be a simple questions but they have been bugging me.
>
> 1. I have two diagnostic groups that I want to compare controlling
> for gender and age. I am entering them in Qdec with diagnosis and
> gender as discret
it does not look like you changed the command line. Also, please cut and
paste the info into the email instead of taking a snapshot.
thanks
doug
On 02/04/2013 07:26 AM, Richter, Julia wrote:
> This doesn't work either (see attachment) :(
>
> -Ursprüngliche Nachricht-
> Von: Douglas N Gre
Hi Sophie, can you cut and paste the actual command line that you are
using? I don't know what all the symbols mean.
doug
On 02/04/2013 08:15 AM, Sophie Maingault wrote:
>
> Hello everyone !
>
> I want to use qdec so I tried to smooth the subjects with the
> following command: recon-all -s < t000
No, sorry, the labeling of all structures is done simultaneously.
doug
On 02/04/2013 08:20 AM, Hemant Bokil wrote:
> Hi all,
> Is there a way to get freesurfer to annotate only certain selected
> structures (e.g. basal ganglia). I suspect not, since the underlying
> model involves spatial relatio
Hi Sophie, you can only run one subject at a time. What is your command
for one subject?
doug
On 02/07/2013 11:41 AM, Sophie Maingault wrote:
> Actually, I have more than 450 subjects but I will give an example with less
> subjects (here 3 subjects). So the command line that I run is : recon-al
Hello,
I need to download an older version of freesurfer (Version 5.0) on a Mac
Lion 10.7.5. In the archives I don't see a file for Lion, just Leopard and
Tiger. Is it possible that either of these will work for Lion? Also, are
there any step by step instructions on how to install?
Thanks!
Krista
that link should work now
doug
On 02/07/2013 12:53 PM, Uri Hasson wrote:
> Dear Doug,
>
> We're still using version 5.1 for a pipeline, and need to send
> surface-based measures (volume, area, thickness) to a standard space
> for whole-brain analysis. I read you had a patched version of
> mris_p
Hello Krista,
freesurfer v5.0 does not have a Lion build. Im fairly certain Lion did not
even exist when 5.0 was released. I suggest you give the Leopard build a
try, I *think* it will work, but I haven't tested it.
If you download the the .dmg file the install should be fairly self
explanatory.
I just noticed their are two Leopards builds... go with the leopard-i686
version.
-Zeke
> Hello Krista,
>
> freesurfer v5.0 does not have a Lion build. Im fairly certain Lion did not
> even exist when 5.0 was released. I suggest you give the Leopard build a
> try, I *think* it will work, but I h
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