Hi FS users,
We've T1 and EPI images collected. For my analysis I want to use FS parcellated
regions (both cortical/sub-cortical regions) as ROIs (Masks) for my functional
images. Would anyone kindly let me know what is the best way to proceed. Cheers,
Sabin
Hi,
Is it possible to get over some 2D representation of the cortex (whether it's
on a plane, on the surface of a sphere, it doesn't matter (although the plane
would probably be easiest to work with)) to get cortical thickness measures
at every location?
Thanks,
--Mohammad
This e-mail
Dear experts
I have created a larger number of labels on the FS_average surface and
performed an FS_FAST analysis. The main goal is to obtain a functional
connectome that contains all the possible correlations between 50 Rois in 100 subjects.
The FS_fast analysis resulted in a
establish a registration between the functional and anatomical with
bbregister, then use mri_label2vol to map the aparc+aseg.mgz into the
function space.
On 01/21/2015 01:52 PM, sabin khadka wrote:
Hi FS users,
We've T1 and EPI images collected. For my analysis I want to use FS
parcellated
My desirable output would be then a .txt file that consists of merely two
columns. The first column is the subject's ID and the second is the CNR value
only, for example:
bruce 1.602
bert 1.555
john_doe 1.666
Thanks in advance.
Cheers,
Jacek
Dnia 21-01-2015 o godz. 20:34 Bruce Fischl
Hi everyone
I don't know if someone had the chance to look at the data we uploaded
for advice to edit the recons (see below).
Thank you so much
Celine
On Fri, 2015-01-16 at 11:43 -0500, Celine Louapre wrote:
Thanks Bruce
The aseg is correct, no ventricule labeled there (I was used to that)
Hi Mohammad,
the thickness can be displayed as a map on any surface we create. We do
create ?h.sphere files by default, so you can use those if you want. If
you'd rather a planar representation you need to make cuts in the inflated
surface and use mris_flatten.
cheers
Bruce
On Wed, 21
Oh, I thought it was already defined. I am referring actually to this thread...
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-August/025251.html
...and, allowing myself to specify my problem, when I type the command
'mri_cnr' what I become in my terminal is something more or less
Hi Jacek
if you give us an example of what the desired output would be for you it
would just be a couple of minutes to put it in the code. Or maybe someone
can post some sed code (or some easy alternative) to parse the CNR out of
the output.
Bruce
On Wed,
21 Jan 2015, Jacek Manko wrote:
Also, i didn't attach the error I got- please see attached.
Thanks!
m
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
Sent: Tuesday, January 20, 2015 4:21 PM
To: Freesurfer support list
You are correct. Note that if you want to compute an average inside of a
label, that you may want to use fMRI data that is unsmoothed (even on
the surface) as this will cause false correlations between labels.
doug
On 01/21/2015 01:16 PM, Jan Willem Koten wrote:
Dear experts
I have created
Hi Everyone,
I have been using both tksurfer and QDEC to view group comparisons of cortical
thickness maps. One advantage of using tksurfer has been the ability to view
various measures such as mean, tval, and stderr. Is there any way of viewing
maps other than just the mean
You will need a 4 group FSGD. The interaction would be contrast 7 on the
4G web page
doug
On 01/21/2015 09:38 AM, lindsay hanford wrote:
Hello Doug,
Thank you for your reply. I misused the word contrast, when I should
have said design matrix. It looks at though I should be able to look
how do you want to define CNR?
On 01/21/2015 06:21 AM, Jacek Manko wrote:
Dear All,
I have been wondering if there is a way (already implemented in the
FreeSurfer) to export CNR measurement outputs to seperate file, like a table
or someting. If not, it will possible only via some pretty
actually if you run mri_cnr with -l out.log it will write a line to out.log
of the form:
gray_white_cnr gray_csf_cnr white_mean gray_mean csf_mean sqrt(white_var)
sqrt(gray_var) sqrt(csf_var))
so you would create one file for each subject. You could then run a for
loop over your subjects to
would something like this work?
set cnr = `mri_cnr $SUBJECTS_DIR/$subject/surf
$SUBJECTS_DIR/$subject/mri/norm.mgz | grep total | awk '{print $4}'`
echo $subject $cnr yourfile
On 01/21/2015 02:46 PM, Jacek Manko wrote:
My desirable output would be then a .txt file that consists of merely
Thank you for you help! Yes the contrast 7 in the group 4 example makes
complete sense. However, I am still left with not being able to control for
the effects of another categorical variable.
For example I can look at the interaction of Group X Score, but for this I
need to remove the categorical
If you run it with --help you'll see several examples.
On 01/21/2015 03:21 PM, sabin khadka wrote:
Hi Doug- Thanks for the reply. Would you mind elaborating on how
exactly to use mri_label2vol to map the aparc+aseg.mgz into the
function space ( I could not find the correct syntax that should
Hi all,
I recently installed freesurfer on my mac, and I'm having a small problem with
freeview. If I load a segmentation file, and then try to associate it with a
custom color lookup table, freeview stops responding. Even if I was to use an
exact copy of
Hi Doug- Thanks for the reply. Would you mind elaborating on how exactly to use
mri_label2vol to map the aparc+aseg.mgz into the
function space ( I could not find the correct syntax that should be used)?
Also, what should i do if I want individual masks for each ROI?
Cheers,
Sabin Khadka
The Group by Score interaction.mtx is indeed
0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 0
On 01/21/2015 03:26 PM, lindsay hanford wrote:
Thank you for you help! Yes the contrast 7 in the group 4 example
makes complete sense. However, I am still left with not being able to
No, sorry.
doug
On 01/21/2015 01:02 PM, Leyden, Kelly wrote:
Hi Everyone,
I have been using both tksurfer and QDEC to view group comparisons of
cortical thickness maps. One advantage of using tksurfer has been the
ability to view various measures such as mean, tval, and stderr. Is
there
I can confirm this bug on Mac (It does not happen on Linux). I'll look
into it.
Best,
Ruopeng
On 01/21/2015 03:11 PM, Mateus Aranha wrote:
Hi all,
I recently installed freesurfer on my mac, and I'm having a small
problem with freeview. If I load a segmentation file, and then try to
thank you
smoothing=shit;
cheers jan
Gesendet:Mittwoch, 21. Januar 2015 um 20:01 Uhr
Von:Douglas N Greve gr...@nmr.mgh.harvard.edu
An:freesurfer@nmr.mgh.harvard.edu
Betreff:Re: [Freesurfer] Correspondence between label vertex number and time course
You are correct. Note that if you
Dear All,
I have been wondering if there is a way (already implemented in the FreeSurfer)
to export CNR measurement outputs to seperate file, like a table or someting.
If not, it will possible only via some pretty advanced bash scripting, am I
right? If so, has anyone some experience with that
Hello Doug,
Thank you for your reply. I misused the word contrast, when I should have
said design matrix. It looks at though I should be able to look at an
interaction effect between two variables but ignore another. In the case of
the example
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V
26 matches
Mail list logo
