Dear Freesurfer experts,
I tried to create high resolution ribbon from pial and white surfaces.
Actually I found this question in mailing list but the answer was not
clear. I have a register.dat file and white and pial surfaces. My aim
is to create a high resolution ribbon from those by using
r
Hi Rouhollah
what resolution do you mean? You can use mris_fill to fill the interior
of the white and pial surfaces at whatever resolution you want, then
compute the AND of the two volumes in matlab, or perhaps using mri_mask or
something similar.
cheers
Bruce
On Thu, 13 Dec 2012, Rouhollah
Hi Patrice
you can use mris_register with the -1 switch to indicate that the target
is a single surface not a statistical atlas. You will however still have to
create the various surface representations and geometric measures we expect
(e.g. ?h.inflated, ?h.sulc, etc). If you can convert yo
Hello All,
As recently as September we were downloading our fMRI scanning data from
Bourget by
setting the following freesurfer environment:
source /usr/local/freesurfer/nmr-stable51-env
and then unpacking and converting the data to Nifti format using the
"unpacksdcmdir" commands:
unpackscdcmdir -
Hi Thackery, are you running locallyin the Martinos Center? When I
source that env, I have access to unpacksdcmdir. what is your
$FREESURFER_HOME variable set to (after sourcing)?
doug
On 12/13/2012 11:45 AM, thack...@nmr.mgh.harvard.edu wrote:
> Hello All,
> As recently as September we were down
I ran Freesurfer on OASIS longitudinal data with the longitudinal
pipeline. I want to work with the full brain image (with gray level
intensities) which is intensity normalized and skull stripped and all the
timepoints of a subject are rigidly registered to the 1st time point. There
were many brain
Hi Prasanna, the norm.mgz sounds like the best fit. Though I'm not sure
what you mean by all the images registered to the 1st time point. If you
are doing a longitudinal analysis, then following the longitudinal
stream will result in a set of norm.mgz's that will be in alignment (but
not to the
Hi FS users,
We've generated surfaces using FS v4.4 and would like to determine total brain
tissue volume for each of our cases. Would this correspond to the 'Brain
Segmentation Volume' which is standard in the output aseg.stats file.
How is the 'Brain Segmentation Volume' determined, and
Hi Jim, in 4.4, the Brain Segmentation Volume is basically just an
adding up of the volumes in aseg.stats, but it includes ventricles, so
you would need to subtract those out. Newer versions of FS have a
BrainSegVolNotVent which is the volume of tissue.
doug
On 12/13/2012 12:32 PM, Alexopoulos
Hi Julia, I don't think it looks terrible (unfortunately:). You might
try increasing the smoothing level (maybe 10 fwhm).
doug
On 12/12/2012 08:02 AM, Julia Foecker wrote:
> Hey Doug,
>
> thanks for your reply. I tried now the polar angle mapping for the left
> hemisphere and I got the figure a
On 12/12/2012 09:42 AM, octavian lie wrote:
> Dear All,
> Excuse the basic nature of these quetions. I coregistered 2 analyze
> volumes in SPM (pre and post resection MR scans for same patient) with
> cost function masking. I imported the preresection scan in Freesurfer,
> and processed it with
Doug,
Thanks. When I add up all 49 fields in the aseg.stats I don't get the same
number (actually larger)
as the 'Brain Segmentation Volume'.
v4.4/aseg.stas also includes a 'Brain Segmentation Volume Without Ventricles'.
I presume we can use this, and subtract out the CSF for total brain tissue?
Hi Cedric, when you view it marsbar, are you viewing it on avg152T1.nii?
Do avg152T1.nii and DLPFC.nii have the same geometry? To check, look at
the qform matrix with:
mri_info --vox2ras avg152T1.nii
mri_info --vox2ras DLPFC.nii
and make sure that they have the same number of rows, cols, slices
Hi Alexopoulos,
See wiki page below for definition of morphometry stats.
https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
-Louis
On Thu, 13 Dec 2012, Alexopoulos, Dimitrios wrote:
> Doug,
>
> Thanks. When I add up all 49 fields in the aseg.stats I don't get the same
> number (actuall
Hi Bruce,
Thanks for your prompt answer!
I have started working on your suggestions...it has worked so far, but I
am reaching a small problem. Let us say I have two subjects, Subject1
and Subject2. For each, I was able to generate lh.orig, and subsequently
lh.smoothwm (and lh.aread, lh.curv), th
I knew I would forget something :)
mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated
Bruce
On Thu, 13 Dec 2012, Patrice Koehl wrote:
>
> Hi Bruce,
>
> Thanks for your prompt answer!
>
> I have started working on your suggestions...it has worked so far, but I
> am reaching a s
Thanks! Now it is working!
Final questions...I hope:
- Does the vertex order remain the same in all the successive files?
If the vertices are in the order V1,., VN in lh.orig, will
I find them in the same order in lh.sphere, and then in lh.sphere.reg?
- I am trying to use tksurfer to vi
yes, they are all the same surface topologically, and the face and vertex
indices are invariant within subject and hemisphere
On Thu, 13 Dec 2012,
Patrice Koehl wrote:
>
> Thanks! Now it is working!
>
> Final questions...I hope:
>
> - Does the vertex order remain the same in all the successive f
Hi Jorge,
Thank you for your careful explanations, it did help :)
Regards, -Ting
On Wed, Dec 12, 2012 at 11:35 PM, jorge luis wrote:
> Hi Ting
>
> Just use the default procedure. We limited the number of iterations for
> the estimation procedure to 20 for the mass-univariate analysis. If the
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