Mmmh...
So, would it be possible to create a series of trials beforehand (which I
actually have) and then let the optseq2 algorithm allocate the adequate amount
of null events at optimal time points (iteratively of course)?
Tilman
Von: Douglas N Greve [gr.
Hi,
I usually re-process, to be on the safe side.
But,
the base run (and that is where you got stuck) is very similar to the
cross sectional run, except for the beginning where the template image
and maps are created, so if you passed that step, you should be able to
treat is as you would with a c
Hello to everyone!
Hope the new month is bringing better weather to all of you.
I am trying to load new data. I cd-d to the location of the files (.hdr and
.img). Now I am trying to convert the data. It doesn't recognise the
information. I've manually created the files JS, MRI, and Orig within to
Hello freesurfers,
we have several data processed (with recon-all) using FreeSurfer v.4.3.1,
but we are thinking in moving to v.4.5. Do we have to re-run recon-all again
for all the subjects, or can we just run the new features implemented in the
new version (If so, is there any 'easy way' to do i
did you try giving it the .img file as input and the .mgz as output?
On Tue,
2 Mar 2010, Janani Dhinakaran wrote:
> Hello to everyone!
> Hope the new month is bringing better weather to all of you.
>
> I am trying to load new data. I cd-d to the location of the files (.hdr and
> .img). Now I am
Dear FreeSurfers,
in the FreeSurfer cortical parcellation procedure, a volume measure is
calculated for the lateral orbitofrontal cortex and in my study population I
indeed do find a significant group difference in the volumes of this region.
However, there certainly is signal loss of the MR si
Hi Cindy,
it depends on the bandwidth of the imaging sequence. We use multi-echo
mprage to avoid this type of thing. Do the surfaces look accurate in
these regions? I can imagine that it would affect thickness more than
surface area. Have you checked which parameter dominates your volume
chan
Yes, just did.
This is what I got.
s0964...@cric-0012:~/Desktop/Newdata/RAW_DATA/1_1$ mri_convert
Desktop/Newdata/RAW_DATA/1_1/**^**_1_1_1.img
Desktop/Newdata/JS/mri/orig/001.mgz
mri_convert Desktop/Newdata/RAW_DATA/1_1/**^**_1_1_1.img
Desktop/Newdata/JS/mri/orig/001.mgz
$Id: mri_c
are there really all those '*'s in the name? And the ^? Those
are probably messing things up.
On Tue, 2 Mar 2010, Janani Dhinakaran
wrote:
> Yes, just did.
> This is what I got.
>
> s0964...@cric-0012:~/Desktop/Newdata/RAW_DATA/1_1$ mri_convert
> Desktop/Newdata/RAW_DATA/1_1/**^**_1_1_1
I'm not sure what you mean. When the sphere.reg is registered across
subjects, it is sufficient to register the wm surfaces.
doug
Matt Glasser wrote:
>
> Hi,
>
>
>
> I am wondering if there is a way to apply the default surface based
> registration that is done during recon-all to surfaces ot
No, but that's an interesting idea, and might not be too hard to
implement. So you already have a sequence, you just want nulls to go in
them?
doug
Gaber, Tilman wrote:
> Mmmh...
> So, would it be possible to create a series of trials beforehand (which I
> actually have) and then let the optse
Hi Doug,
Thanks for your response. How does one go about getting registered white
matter surfaces then? I would like all of the surfaces to be registered so
that they have the same number of nodes in the same places across subjects.
Thanks,
Matt.
-Original Message-
From: Douglas N Gre
Oh, that's not such an easy thing to do. We can only map values from one
subject to another. I know what you are describing, and it would be nice
to have. I'm not sure how possible it is as the density of the nodes
changes from subject to subject at various locations in order to reflect
the ana
Hi Matt,
you could use mri_surf2surf to map the fsaverage surface to any subject.
We always avoid doing this as we want uniform sampling in the subject's
space, and were willing to make the engineering more difficult to preserve
this.
cheers
Bruce
On Tue, 2 Mar 2010, Douglas N Greve wrote:
Hi Gonzalo,
this is one of the reasons we use the surfaces for cortex instead of the
aseg. The surfaces look for for this sujbect, so why not just use them?
Bruce
On
Tue, 2 Mar 2010, Gonzalo Rojas Costa wrote:
> Hi:
>
> In a patient, I got a bad cortex segmentation... I try to adjust the skull
Hi Doug and Bruce,
I am somewhat surprised by your responses, given that we do what I need done
with Caret all the time. I wonder if I am not explaining myself clearly or
not understanding your responses (Donna, perhaps you can help?). In Caret,
one does a landmark-based registration of the sphe
Hi all,
I'm about to start writing up a paper, and was curious as to whether there is a
standard figure displaying the Desikan parcellations that is floating around
out there, and also whether or not there is a standard blurb describing QDEC's
GLM analyses. Thanks!
Nathan
___
Hello,
I looked at the results from stage 3 and found out it has 1100 regions (we
might not use qdec since we have many other variables to control). But it is
beyond manageable levels. What we want might two things:
The first one might be a general measure of thickness (or volume) of each
Matt,
I think we just do things differently. We adopted Ziad Saad's concept
of a standard mesh. (Before Ziad conceived it, we didn't do this,
either.) But not everyone does this. My mental model of how others do
things is poor. I recall using mrisp_paint to get some scalars on our
PALS su
Hi, Bruce,
We want calculate the four major cortical lobe volumes, i.e. frontal, parietal,
temporal, and occipital, to see the relationship between them and some ROIs. I
did fully run recon-all, but not clear which file should be used and what
cortical areas should be included in these four
Thanks Donna for the explanation of my confusion.
I am wondering if there is any way I could make use of the Freesurfer
registration and then get things into Caret where I could do what I want?
For example, is there any way, given a registered and unregistered sphere of
a given subject that we c
Hi Matt,
I think that is all doable using mri_vol2surf, mri_surf2surf and
mri_surf2vol. The deformation fields all live on the surface of the sphere,
so there is no volumetric deformation to apply. It's also all subject to
atlas. You could pick an individual subject and compose forward and inve
David Salat was going to draw these, but I'm not sure if he ever did.
David?
On Wed, 3 Mar 2010, caoaize wrote:
Hi, Bruce,
We want calculate the four major cortical lobe volumes, i.e. frontal, parietal,
temporal, and occipital, to see the relationship between them and some ROIs. I
did fu
Hi,
I am analyzing structural data (analyze format).
How can I run autorecon with one image?
A similar question was already asked on 14 Jun 2008, but I couldnt find how
to run it.
Thanks,
Amy
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
what do you mean by "one image"? If one volume, then just run it
normally, something like
recon-all -s subjectname -i volume.img -all
We recommend that people not use analyze because analyze does not store
information about orientation, so you could get a left-right reversal.
doug
ay...@haski
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