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Hi,
Just a quick question to the Freesurfer creators : how could I cite the
bbregister command line in an article ? I didn't find the correct
article in the Freesurfer Wiki.
Thanks,
--
Christopher Coello, Ph.D.
Preclinical PET/CT unit
Institute of Basic Medical Sciences
Faculty of Medicine, U
Hi chikku. Yes all steps are necessary (see the description on the wiki).
First all time points need to be processed cross sectionally.
Best Martin
Varghese Chikku wrote:
>Martin,
>Forgive my ignorance and sorry to pester you. From what you said in
>the
>mail,
>*The base is like an additional
Doug,
Do you mean that the functional file mean.nii is not aligned
with the structural data? I know that -- o means resample mov and save as
outvol. Why do you need to resample the mean.nii? To align with structural data
in freesurfer? If you do that, will the outvol be able to la
Accurate and robust brain image alignment using boundary-based
registration, D. Greve and B. Fischl, NeuroImage, Volume 48, Issue 1, 15
October 2009, Pages 63-72.
it's on the wiki
On Fri, 1 Mar 2013, Christopher wrote:
> Hi,
>
> Just a quick question to the Freesurfer creators : how could I cit
I have sent the attachment mentioned in the mail below via mail drop.
On Thu, Feb 28, 2013 at 4:28 PM, Blessy M wrote:
> The skull stripped image using FS did not look very good, I am not sure if
> this was the result of skullt stripping or the fact that the volume was
> more than 256^3 (and use
Hi,
If I want to use epi_reg, what do I need to do for the environment in fsl? It
says that it's not recognizing the function bbr. How do find the path to BBR in
/usr/pubsw?
Thank you very much.
Helen
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what is epi_reg? Is that an FS program?
On 03/01/2013 02:19 PM, Chen, Xiaoyan wrote:
> Hi,
>
> If I want to use epi_reg, what do I need to do for the environment in fsl? It
> says that it's not recognizing the function bbr. How do find the path to BBR
> in /usr/pubsw?
>
> Thank you very much.
>
Hi Helen
it's not called bbr, it's called bbregister.
cheers
Bruce
On Fri, 1 Mar 2013, Chen,
Xiaoyan wrote:
> Hi,
>
> If I want to use epi_reg, what do I need to do for the environment in fsl? It
> says that it's not recognizing the function bbr. How do find the path to BBR
> in /usr/pubsw?
>
Doug,
epi_reg is using BBregister with FSL. In FSL5 they incorporated
the tool your guys developed. The following is the error message
[mi2b2:OAEAA005] (nmr-stable5.1-env) epi_reg --epi=meanuf-ep2d-18-0001.nii.gz
--t1=MPRAGE1.nii.gz --t1brain=MPRAGE1_manual2.nii.gz --out=epi2struct
oh, this is the FSL reimplementation of Doug's algorithm (they loved it
so much they had to have their own!). You'll need to ask them about it.
I'll cc MJ so he can chime in.
cheers
Bruce
On Fri, 1 Mar 2013, Chen, Xiaoyan
wrote:
> Doug,
> epi_reg is using BBregister with FSL. I
Hi Helen, that is probably their implementation of BBR, so you should
contact them directly.
doug
On 03/01/2013 02:28 PM, Chen, Xiaoyan wrote:
> Doug,
> epi_reg is using BBregister with FSL. In FSL5 they incorporated
> the tool your guys developed. The following is the error mess
Doug,
I'm trying to do the same thing as Ben, i.e., show a FS surface (e.g.
'lh.white') in the same space as the MRI ('T1.mgz'). I have been
studying the wiki page (and linked PDF) but I'm a bit lost. Is there an
easy way to get an affine transform that maps the surface to the
coordinate syste
Dear all,
Thank you so much! It works now.
Helen
On Mar 1, 2013, at 2:41 PM, Mark Jenkinson wrote:
> Hi,
>
> It looks like your installation isn't right - you need FSL5.0 or higher for
> this to work. If not I would expect it to complain about: "Unrecognised cost
> functi
Hi Katie, the problem is that eventtypes 1 and 2 are synchronized 32 sec
apart. What this means is that they are effectively one event if you set
the time window longer than 32 sec (you have it set to 34). There is no
way around this. If you want a longer window, use 30 sec (32 might work).
doug
On 02/27/2013 03:13 PM, Kristina Nalbandian wrote:
> Hello,
>I am running qdec group analysis on my patient data. I am studying
> the differences between two Epilepsy onset types and have a few
> questions.
>
> 1) I select "subtype" as my discrete variable and "duration" as my
> continuous
Hi Katharina, is there really a problem with the output going into the
SUBJECTS_DIR? If so, you can create a separate SUBJECTS_DIR for each
project. Inside of each SUBJECTS_DIR you can then create a symbolic link
back to the original SUBJECTS_DIR, linking only the subjects you want in
that pro
Hi list,
Where Can I find basic information about entorhinal cortex analysis?
Thank you very much.
Stefano
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The information in this
Hi Stefano
look on the wiki and search for entorhinal. In particular, this paper:
http://surfer.nmr.mgh.harvard.edu/pub/articles/YNIMG6159.pdf
describes how we estimate the location of EC in vivo
cheers
Bruce
On
Fri, 1 Mar 2013, std...@virgilio.it wrote:
> Hi list,Where Can I find basic infor
Ok, I understand that, except that all of my runs are like that, but only a
few of them errored out. Why is that?
Katie
On Fri, Mar 1, 2013 at 3:38 PM, Douglas N Greve
wrote:
> Hi Katie, the problem is that eventtypes 1 and 2 are synchronized 32 sec
> apart. What this means is that they are eff
I don't know. It might be that the other ones are close to being badly
conditioned and just don't meet my (arbitrary) threshold.
doug
On 03/01/2013 06:30 PM, Katie Bettencourt wrote:
> Ok, I understand that, except that all of my runs are like that, but
> only a few of them errored out. Why is
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