Hi all,
If someone can give me help, it would be greately appreciated.
in csurf GUI,
I choose "New Functional", and I give it a name.
(1) The name is entirely new for analysis or is it the directory that
contains functional scan.
If I give it a name, it asks for
"Now, locate the single subjec
Hi all,
I would like to overlay multiple functional datasets onto the same flattened
structural image. How do I go about this?
Thanks
Ruth
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Hi,
I am having problems with functional overlays onto my anatomical. When I go to
set functional sessions directory an Alert message appears saying :
session:left_down (functional name) scripts subdir not found
using /tmp make scripts dir to save session_specific params.
What exactly is this r
Hi everyone
Could I divide the values of a functional overlay
volume by a known constant in tkmedit or using any
other function of freeSurfer?
thanks
abel
LLama Gratis a cualquier PC del Mundo.
Llamad
Hi Nam,
what format are your functional data in? You should be able to load them
directly in tksurfer using file->load functional overlay.
cheers,
Bruce
On Thu, 11 Nov 2004, Joongnam Yang
wrote:
Hi all,
If someone can give me help, it would be greately appreciated.
in csurf GUI,
I choose "New F
Hi Bruce,
I co-registered functional and structural images using SPM, the results of
which looked normal.
Then, I used spmmat2register to produce register.dat file.
But "register.dat" contained only following two lines.
subjectname
0.3000
It is supposed to have 8 lines.
Could you guess what we
Use tkregister2 to create the register.dat. Run it with --help to get
more info. spmmat2register is obsolete.
doug
On Fri, 12 Nov 2004, Joongnam Yang wrote:
> Hi Bruce,
>
> I co-registered functional and structural images using SPM, the results of
> which looked normal.
> Then, I used spmmat
I'll leave this for Doug.
Bruce
On Fri, 12 Nov 2004, Joongnam Yang wrote:
> Hi Bruce,
>
> I co-registered functional and structural images using SPM, the results of
> which looked normal.
> Then, I used spmmat2register to produce register.dat file.
> But "register.dat" contained only following tw
Thanks Doug,
When I run
tkregister2 --targ structuralimage --mov functionalimage --reg register.dat
I got the following error.
==
target volume X.img
movable volume XX.img
reg file register.dat
LoadVol1
$Id: tkregister2.c,v 1.22 2003/11/05 21:30:50 gr
Tell it to initialize the registration based on the header
information. To do this add --regheader to the command-line. Once the
register.dat exists, do not use --regheader unless you want to
overwrite your results.
On Fri, 12 Nov 2004, Joongnam Yang wrote:
> Thanks Doug,
>
> When I run
>
Thanks Doug,
So,
"structural data registration"
"functional data registration"
"co-registration"
have to be done separately? How do I do the first two?
The manual is pretty murky on that. Please enlighten me...
I am trying to do functional overlay using csurf and there are so many
hidden things w
Actually, I don't know what the first two mean either. I don't think
you need them. Once you have the register.dat, then you're ready to go.
On Fri, 12 Nov 2004, Joongnam Yang wrote:
> Thanks Doug,
>
> So,
> "structural data registration"
> "functional data registration"
> "co-registration"
Hi Ruth,
can you explain what you mean? You can load overlays into different
layers with file->load functional overlay, and switch between them using
the view menu.
cheers,
Bruce
On Tue, 11 Jan 2005
[EMAIL PROTECTED] wrote:
Hi all,
I would like to overlay multiple functional datasets onto the
hi all -
i've succeeded in displaying FSL z-maps on an inflated brain. however,
i'm trying to find a way to display the overlap between two z-maps. i
was able to get one to display in red, and the other in blue, with the
overlap being purple. however, this doesn't look very convincing, and
i
Hi,
I need to overlay some functional imaging data onto a structural scan to create
some figures. How would I do this?
I tried an older tutorial but it seems the files don't exist anymore in the
tutorial dataset
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization). However
the
We don't have explicit tools to do this, but you can use matlab
In matlab, you can load the overlay with
a = MRIread('youroverlayfile');
a.vol = a.vol * constant;
MRIwrite(a,'yournewoverlay.mgh'); % or use .nii for nifti
abel cruz vadell wrote:
Hi everyone
Could I divide the values of a
You can load the surface maps into matlab. If they are stored in .w
format, then you can
[w,v] = read_wfile(wfname);
% w - vector of surface values
% v - vector of vertex indices (0-based)
You can also compute the overlap in the volume and then paint that.
mri_vol2surf uses nearest ne
Hi Bryan
have you done freesurfer recons on the anatomicals? If so, you can use
bbregister and mri_vol2surf to map the functional data onto the surface.
cheers
BruceOn
Sun, 28 Sep 2014, Chiu, Bryan (PHTH) wrote:
> Hi,
> I need to overlay some functional imaging data onto a structural scan to
>
Hi,
We are having problems with freesurfer 2004 to overlay the functional .w
or .bfloat files onto the volume. It is not a problem to load the data
onto the surfaces eg flat map, but we cannot set the functional onto the
volume images.
Does someone know how to do this in freesurfer version 2004.
Thanks, Bruce.
When I did successfully using csurf and tkmedit (I will try tksurfer later,
though),
I saw functional data overlaid onto structural data.
Question: I was expecting some activated regions for my retinotopy data, but
all I see is a large green or red contours. Is this what freesurfe
We are having problems with freesurfer 2004 to overlay the functional .w
or .bfloat files onto the volume. It is not a problem to load the data
onto the surfaces eg flat map, but we cannot set the functional onto the
volume images.
Can you be more specific? Do you just need instructions, or are you
You can't overlay .w files onto a volume (surfaces only). Try looking at
tkregister2 --help to get more info on how to create registration
matrices for use with overlaying.
doug
Ruth Smans wrote:
>
> Hi,
>
> We are having problems with freesurfer 2004 to overlay the functional .w
> or .bfloat
Hi,
I have another silly question. When a functional overlay (say, log p-value
map) is loaded to tksurfer, how exactly are the surface vertex values
computed? using simple interpolation of the loaded map? or is it something
more fancier, like looking along the normal of each surface face and takin
Hi shay
Are you using mri_vol2surf to sample it onto the surface before displaying in
tksurfer? If so, you get to choose how to sample and interpolate?
Cheers
Bruce
On Jun 2, 2012, at 9:43 PM, Shay Ohayon wrote:
> Hi,
>
> I have another silly question. When a functional overlay (say, log
Dear Bruce,
I see, so you would recommend to use it with "--projfrac 0.5".
Thanks for your help.
-- Shay
On Sat, Jun 2, 2012 at 7:19 PM, Bruce Fischl wrote:
> Hi shay
> Are you using mri_vol2surf to sample it onto the surface before displaying
> in tksurfer? If so, you get to choose how to sam
Hi Shay,
not necessarily. It depends what your goal is. --projfrac 0 for example
will minimize the chances of an activation spreading across the banks of
a sulcus.
cheers
Bruce
On Sun, 3 Jun 2012, Shay Ohayon wrote:
Dear Bruce,
I see, so you would recommend to use it with "--projfrac 0.5".
Hi Dear FreeSurfers,
I'm using the new version of FreeSurfer to process retinotopic data. I can
view the finial results of eccen, polar and fieldsign on the occiptal
patch.
Now I want to overlay another block designed activations onto the fieldsign
patch with file---load overlay--select the corres
Are you sure the viewing threshold is set correctly for that data?
Check out the View->Configure->Overlay dialog box and try changing the
values.
On Wed, Oct 04, 2006 at 03:22:54PM +0200, [EMAIL PROTECTED] wrote:
> Hi Dear FreeSurfers,
>
> I'm using the new version of FreeSurfer to process retino
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