overwrite the old one if you want.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Guerreiro Fernandes-3,
F.D. (Francisco David)
Sent: Sunday, February 20, 2022 5:55 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] sulc surface error: unit mismatch between
External Email - Use Caution
Dear FreeSurfer Developers,
I'm attempting to correlate the sulcal depth information present in the ?h.sulc
files with activation in particular brain regions during an overt language
task in an fMRI paradigm. For this matter, a dataset was gathered
External Email - Use Caution
I should have mentioned that the HCP data have been processed using
FS5.3HCP. If we know which code/script generates sulc files, we can try to
dig out the code to find the scaling factor.
On Thu, Nov 12, 2020 at 9:46 PM Reza Rajimehr wrote:
> Thanks
External Email - Use Caution
Thanks Doug! It would be great to know what the exact scaling factor is.
The HCP data have been processed/analyzed using FS5.3. We have a set of new
subjects that have been processed using the new version of HCP pipeline
which is based on FS6.0. Since w
I think it is probably just scaling, but it has been a long time since
5.3 and 6.0
On 11/9/2020 10:10 AM, Reza Rajimehr wrote:
External Email - Use Caution
Hi,
In the .sulc files, the range of sulcal depth values are very
different (about 10 times higher) in Freesurfer v6 compared t
External Email - Use Caution
Hi,
In the .sulc files, the range of sulcal depth values are very different
(about 10 times higher) in Freesurfer v6 compared to Freesurfer v5.3. Is
there just a simple scaling factor here, or the procedure for calculating
sulcal depth has been changed
-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: 29 September 2015 14:40
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Sulc value of given Tal coordinates
when you load the fsaverage surface into
College London
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: 29 September 2015 14:40
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Sulc value of given Tal coordinates
when you load
reesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: 28 September 2015 23:15
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Sulc value of given Tal coordinates
>
> You can also map the sulc or curv to fsaverage. The coordinates (in freeview
>
edu
Subject: Re: [Freesurfer] Sulc value of given Tal coordinates
You can also map the sulc or curv to fsaverage. The coordinates (in freeview or
tksurfer) are in MNI305 coordinates which are pretty close to Tal.
doug
On 09/28/2015 05:26 PM, Rudolph Pienaar wrote:
> Hi Karen --
>
> A given F
You can also map the sulc or curv to fsaverage. The coordinates (in
freeview or tksurfer) are in MNI305 coordinates which are pretty close
to Tal.
doug
On 09/28/2015 05:26 PM, Rudolph Pienaar wrote:
> Hi Karen --
>
> A given FreeSurfer surface can be thought of as a triangular mesh. This
> mesh
Hi Karen --
A given FreeSurfer surface can be thought of as a triangular mesh. This
mesh contains many "points" (i.e. the vertex points of the constituent
triangles).
Each of these mesh vertex points contains many internal values, i.e. the
x, y, z position of the point, the normal to the surfa
Hi
I am not a Freesurfer expert or Matlab connoisseur. I am trying to find out how
to get the Sulc and Curv value for a given tal coordinate. I was told that
you load it in Matlab using read_curv, but how exactly do I do this, what does
they syntax look like?
I can see in the help this: [cur
Thank you!
> Hi Angela
>
> you can load it into matlab with read_curv. If you have the surface and
> the
> tal xform (or transform the surface before loading it into matlab) you can
> find the point on the surface that is closest to a given tal coord and
> read
> out the sulc at that point
> cheer
Hi Angela
you can load it into matlab with read_curv. If you have the surface and the
tal xform (or transform the surface before loading it into matlab) you can
find the point on the surface that is closest to a given tal coord and read
out the sulc at that point
cheers
Bruce
On Wed, 23 Sep 20
Hi all,
is there any way (different from manually looking in tksurfer) to know the
value of 'sulc' (or other) in a particular point Talaraich xyz of a
subject?
Thank you!
Angela
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it was in the recon papers (NeuroImage, 1999)
On Sat, 30 May 2009,
Zhangyuanchao wrote:
Dear Mr or Ms,
Thanks a lot for your previous help!
In freesurfer wiki, I notice the description of 'sulc', that is how far removed a particular
vertex point on a surface is from a hypothetical "mid-sur
Dear Mr or Ms,
Thanks a lot for your previous help!
In freesurfer wiki, I notice the description of 'sulc', that is how far removed
a particular vertex point on a surface is from a hypothetical "mid-surface"
that exists between the gyri and sulci."
I am still not quite clear about sulc and ho
Rudolph, many thanks for the additional details.
Just a follow-up question (or two):
1. Short stubby gyri might have the following morphometric
properties?
a) Short feature: shallow sulcal depths would be expected to have
sulc values hovering around the mean surface (e.g. around 0) in
David,
qdec output data is found in your $SUBJECTS_DIR/qdec directory. It is not
in text format, as it is per-vertex data. The file 'sig.mgh' is the main
significance result file. mris_convert can be used to convert that to
text format if you need values at each vertex.
Nick
>
> Dear freesurf
Dear freesurfers,
i m running an analysis using qdec trying to find the group difference between
healthy subjects and MCIs according to their sulc parameter.
My question is, is there an output file with the statistics results as text
file and if so can u please tell me where is it located?? my
nt of Psychology
The University of Melbourne
[EMAIL PROTECTED]
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Thu 5/01/2006 12:42 AM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] .sulc in tksurfer
yes, that makes sens
ECTED]
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Thu 5/01/2006 12:42 AM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] .sulc in tksurfer
yes, that makes sense.
On Wed, 4 Jan 2006, Fornito, Alexander wrote:
> Hi Bruce,
> I'm t
yes, that makes sense.
On Wed, 4 Jan 2006, Fornito, Alexander wrote:
Hi Bruce,
I'm trying to extract thickness for sulci and gyri separately. From what I
understand, positive .sulc values suggest sulci and negative .sulc values suggest
gyri. I'd like to play around with this distinction (e.g.,
Hi Bruce,
I'm trying to extract thickness for sulci and gyri separately. From what I
understand, positive .sulc values suggest sulci and negative .sulc values
suggest gyri. I'd like to play around with this distinction (e.g., call
everything with a .sulc value < .35 'gyral'), and am wandering if
the threshold midpoint in the curvature display just sets where the
transition is from red to green (or light gray to dark gray if using
binary colors)
On Wed, 4 Jan 2006, Fornito, Alexander wrote:
Hi,
Does the 'threshold midpoint' value in tksurfer's curvature display control
correspond to
Hi,
Does the 'threshold midpoint' value in tksurfer's curvature display control
correspond to values in the .sulc file (assuming the .sulc file is loaded), or
are they arbitrary values? For example, if I set the value to .50, does this
make all vertices with a .sulc value of .50 or less lighter
Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Tue 25/10/2005 10:57 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] .sulc and .curv
1. This is the smoothed
1. This is the smoothed mean curvature - the average of the two
principal curvatures smoothed spatially.
2. sulc is the integrated dot product of the movement vector with the
surface normal over the inflation process. Things that move consistently
outwards thus get a positive sign (sulci) and
Hi,
I was just wanting to know more about the .curv and .sulc files. Specifically,
I had three questions:
1 - What exactly does the value assigned to each vertex represent (eg., is it
the curvature of the vertex in the .cuv file?)
2 - How are they derived/calculated?
3 - What do they mean neuroan
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