look in
/Users/lning/subjects/MGH_Ruphert/mri
and
/Users/lning/subjects/MGH_Ruphert/surf
and see if there is any processed data there
On Fri, 3 Aug 2007, Ning Liu wrote:
I think so. It is someone's data. He had created the surfers. I just wanted
to have a look at it.
On 8/3/07, Bruce Fisch
did you run recon-all on this subject?
On Fri, 3 Aug 2007, Ning Liu wrote:
I copied some subjects' data to my computer, but i cannot run the surfer
here is the command line:
tksurfer MGH_Ruphert lh inflated
screen output
surfer: current subjects dir: /Users/lning/subjects
surfer: not in "sc
I copied some subjects' data to my computer, but i cannot run the surfer
here is the command line:
tksurfer MGH_Ruphert lh inflated
screen output
surfer: current subjects dir: /Users/lning/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($sessi
Hello,
I would really like to use a freesurfer surface to display non-human primate
data that I have already put into a standard space and segmented, but I am
having trouble finding information on how to skip many of the initial steps
to this point.
Also, I have seen references to a "-monkey" opt
Keith,
You will need to install the Compatibility standard C++ libraries
for Fedora Core 4. You can get the rpm's here:
http://rpmfind.net/linux/rpm2html/search.php?query=libstdc%2B%2B.so.5
look for Fedora Core 4.
Nick
On Fri, 2007-08-03 at 16:06 -0400, Keith Sudheimer wrote:
> I am runnin
I am running a Fedor Core 4 machine and have installed the CentOS 4 version of
freesurfer. I can run tkmedit and tksurfer. However, I am running into
trouble running trhough
recon-all -s 004FSC -autorecon1
When I get to Nu Intensity Correction (mri_nu_correct.mni) on iteration1,
during volu
Thanks! This sounds very promising and we will try that time using the
code you sent.
As for the current mc data from mri_glmfit, does anyone know if
Freesurfer can give cluster sizes as a function of corrected p-value
like AFNI does?
Thanks,
Rob
Don Hagler wrote:
There is no reason why yo
hmmm, not sure i understand. You can visualize any scalar field in the
volume, so yes. As for the volume, I guess you could create a functional
volume with the value in each voxel the slice # that it is in and just
paint that onto the surface as normal.
cheers,
Bruce
On Fri, 3 Aug 2007, Paul
Hello All,
I have 2 questions I hope someone can help me with. 1) Is it possible to
plot on a surface a set of arbitrary points in the coordinate frame of
an anatomical volume? In other words if I have a set of x,y, and z points
(not voxel indices: e.g. sub-voxel coordinates) can I plot the
There is no reason why you shouldn't be able to get the cut-off size from
monte carlo simulations. It just depends on the program you use to do it.
For example, AFNI's AlphaSim gives cluster sizes as a function of corrected
p-value.
By the way, monte carlo simulations are a waste of time.
Hi,
I was trying to figure out if there is any way to determine the exact
size at which clusters becomes significant given a specified
significance, and it appeared from the mc-corrected overlay that in this
overlay the clusters do not continously change in size but appear
discretely at a giv
Hello,
I found a possible bug in mri_surfcluster, but it may be linked
specifically to average7 and no other srcsubjects (but I haven't checked
that). When I run mri_surfcluster with cluster simulation data, the
size is reported at a seemingly arbitrary number, based on the fact that
the #of
Hello,
We're designing a task that has two pairs of events (4 events total). Each
pair of events has a pair of allowable null intervals associated with it. Is
it possible to use optseq2 to create such a paradigm? Is it appropriate to
use optseq2 in this case at all given these constraints?
___
Dear all,
I'm currently trying to conduct a surface-based group analysis using 1st
level contrast images from SPM5.
I wanted to ask if somebody could tell me if what I'm doing is OK. I
would relly appreciate your help!
I will now describe the procedure:
The functionals of each subject were r
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