Reilly
*Sent:* Wednesday, April 28, 2021 4:30 PM
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] Cortical surface analysis
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Hi Bruce,
Thanks a lot for this. What is the difference between RAS and surface
RAS?
Do I need to convert the surface
M
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Cortical surface analysis
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Hi Bruce,
Thanks so much for your quick reply, I really appreciate your help on this.
I don't understand how to recover the vertex
; Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Ornaith O Reilly
> *Sent:* Tuesday, April 27, 2021 8:02 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Cortical surface analysi
On Behalf Of Ornaith O Reilly
Sent: Tuesday, April 27, 2021 8:02 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical surface analysis
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Hi Bruce,
Yes I read in the patch the way that you're suggesting and I can access the
vino for the flat map
;> patch = read_patch(path_file_name)
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Ornaith O Reilly
> *Sent:* Wednesday, April 7, 2021 2:29 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Fre
surfer support list
Subject: Re: [Freesurfer] Cortical surface analysis
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Hi Bruce,
Thanks so much for your quick reply, I really appreciate your help on this.
I don't understand how to recover the vertex index.
In Freeview I can see the vertex index number. When
...@nmr.mgh.harvard.edu
On Behalf Of Ornaith O Reilly
Sent: Tuesday, April 6, 2021 2:19 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical surface analysis
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Hello FreeSurfer developers,
Thanks a lot for your help. I have initialised the pialxyz the way you
External Email - Use Caution
Hello FreeSurfer developers,
Thanks a lot for your help. I have initialised the pialxyz the way you
suggested and made the flatmap in MatLab using the read_patch function
(screenshots attached). I still don't understand how to convert between
the
On 3/8/2021 11:38 AM, Ornaith O Reilly wrote:
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Hello Freesurfer developers,
I am new to Freesurfer and I'm hoping that someone can help me.
My goal is to be able to visualise electrodes contacts that are on
lying on the cortical surface on a flat map
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Hello Freesurfer developers,
I am new to Freesurfer and I'm hoping that someone can help me.
My goal is to be able to visualise electrodes contacts that are on lying on
the cortical surface on a flat map and a spherical map.
I've run recon-all and
Yes, it will
On 8/7/2020 6:27 PM, Alexopoulos, Dimitrios wrote:
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Hi all,
Does this command calculate the Cortical Surface Area without the
non-cortical Medial Wall??
mris_calc --label ../label/lh.cortex.label lh.area stats
Jim
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Hi all,
Does this command calculate the Cortical Surface Area without the non-cortical
Medial Wall??
mris_calc --label ../label/lh.cortex.label lh.area stats
Jim
The materials in this message are private and may
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OK. Thank you very much.
Sincerely,
Zheng
At 2018-08-13 01:15:26, "Douglas Greve" wrote:
You can break up the aparc annotation into labels (mri_annotation2label), then
create a new annotation with just the insula (mris_label2annot)
On
You can break up the aparc annotation into labels
(mri_annotation2label), then create a new annotation with just the
insula (mris_label2annot)
On 8/12/18 5:17 AM, 郑凤莲 wrote:
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Dear experts,
I an using FS 6.0 for cortical reconstructions. I can show
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Dear experts,
I an using FS 6.0 for cortical reconstructions. I can show whole brain
regions (tksurfer...), as shown in the picture. However, I just want to show
insular region. Is there any way to complete it? I am looking forward to your
Thank you for the input.
Jim
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Friday, October 13, 2017 10:09 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] cortical surface
that is the area of the white matter surface in mm2
On 10/12/17 2:15 PM, Alexopoulos, Dimitrios wrote:
What measure is for the cortical surface area?
The measure in the aparc.stats file states ‘WhiteSurfArea’
Jim
The
>
> Jim
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Thursday, October 12, 2017 5:17 PM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu&g
support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] cortical surface area
oh, sorry, I missed the 5.3 part. YOu can always compute it for a subject
via:
mris_anatomical_stats pial
cheers
Bruce
On Thu, 12 Oct 2017,
Alexopoulos, Dimitrios wrote:
> I don't see
; From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Thursday, October 12, 2017 4:52 PM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] cortic
fer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] cortical surface area
Hi Jim
check the ?h.aparc.pial.stats file. I think the total surface area should be in
there.
cheers
Bruce
On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote:
> Specifically, where in the aparc.stats file (or o
lt output for 'WhiteSurfArea'.
>
> Jim
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Thursday, October 12, 2017 4:16 PM
> To: freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, October 12, 2017 4:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] cortical surface area
mm2
On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote:
>
> What measure is for the cortical surface area?
>
> The measure in the aparc.stats file states 'W
mm2
On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote:
>
> What measure is for the cortical surface area?
>
> The measure in the aparc.stats file states ‘WhiteSurfArea’
>
> Jim
>
>
>
> The materials in this message are
What measure is for the cortical surface area?
The measure in the aparc.stats file states 'WhiteSurfArea'
Jim
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not
Hi Greg
you could threshold then look at Hausdorff distance of the blobs. Or you
could smooth before computing correlation as that will take spatial stuff
into account.
Or if you have a patch that you want to cross-correlate against the rest of
the surface you could do it on the sphere,
Hi,
has anyone created functionality to compare the spatial correlation/similarity
of two patterns in the form of cortical surface overlays. What I am looking at
is a have
scalar at every point on the cortical surface. obviously this is just a list of
vertices with
a scalar value associated
Hi Emma,
Please, see below:
On 13 October 2014 20:11, Emma Thompson vonecono...@gmail.com wrote:
Hi Anderson,
Thank you for your paper. I guess I am confused. I have analyzed my
structural data with qdec, specifically looking at a measure of cortical
thickness and volume. I'm considering
If you are using --qcache, then there is nothing wrong specifically with
the qdec implementation
On 10/13/2014 03:11 PM, Emma Thompson wrote:
Hi Anderson,
Thank you for your paper. I guess I am confused. I have analyzed my
structural data with qdec, specifically looking at a measure of
Hi Anderson,
Thank you for your paper. I guess I am confused. I have analyzed my
structural data with qdec, specifically looking at a measure of cortical
thickness and volume. I'm considering looking at surface area as well but
was told it wasn't a very good measure using qdec, I have no other
Hi Emma,
Could you clarify what would be the disadvantages that you've heard about?
I ask because we've studied and tried to clarify many aspects of the
analysis of surface area in this paper
http://www.sciencedirect.com/science/article/pii/S1053811912002996. Maybe
if there's something not
Hi Donna,
In that same paper we also comment on the differences between
expansion/contraction and absolute areal measurements assessed at each face
of the surface (i.e., facewise), which can, after interpolation, be
converted to vertexwise to facilitate analysis using current tools (e.g.,
Dear Freesurfers,
I recently heard that there are several disadvantages to using a measure of
cortical surface area in Freesurfer, specifically due to conducting a
vertex-wise analysis. Can someone help me understand why a measure of
surface area using this approach might be flawed? Thanks!
Hi Emma,
I might not be the only one who is unsure what you mean by a vertex-wise
cortical surface area measure. Do you mean something like what is illustrated
in figures 2 and 3 here:
http://www.pnas.org/content/107/29/13135.figures-only
… which is similar, but not identical to the local
Dear Freesurfer experts, I am
interested in running cortical surface area on longitudinal data from MRI scans
and run multisubject comparisons (patients vs controls). I would like to ask
you where could I find either a tutorial or a guide for performing
Regarding Winkler et al.:
http://brainder.org/2012/06/02/facewise-brain-cortical-surface-area-scripts-now-available/
On Aug 21, 2012 11:00 PM, Gregory Kirk gk...@wisc.edu wrote:
Hi folks, I wanted to make sure i have everything straight w.r.t. the
surface area measures.
as i see there are 4
Hi folks, I wanted to make sure i have everything straight w.r.t. the surface
area measures.
as i see there are 4 ways implemented ( somewhere ) to do cortical surface
area analysis.
1. areal expansion
2. Local Gyrification Index
3. direct vertex based true surface area glm, Winkler AM et.
Hi Greg, I don't know what areal expansion refers to. If you want to
use area (eg, the area tab in qdec), you should make sure to download
the most recent version of mris_preproc (which performs a jacobian type
correction)
For #1, it might be easier to use mri_surf2surf with the --sval-tal-xyz
option. See the --help for more info.
doug
Bruce Fischl wrote:
1. Yes, just apply the talairach.xfm transform to each vertex. Should be
easy enough to do in matlab using read_surf.m.
2. Yes, this can also be done in
1. Yes, just apply the talairach.xfm transform to each vertex. Should be
easy enough to do in matlab using read_surf.m.
2. Yes, this can also be done in matlab, saving either in curv
(write_curv.m) or wfile format.
On Sat, 22 Oct 2011, Nela Cicmil wrote:
Dear Freesurfer Developers and Users,
Dear Freesurfer Developers and Users,
I have two question(s) about Freesurfer and individual subject's MNI
coordinates:
(1) Having run recon-all to reconstruct the cortical surface for an individual
subject in my study, is it possible to obtain the list of coordinates that
describe the
Hi,
Is there a tool to derive the cortical surface areas of
the cortical structures listed in aseg.stats?
Ed
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The information in
Hi Ed,
the surface areas are usually in the aparc files as they are functions of
the surface models, while the aseg is a volume segmentation.
cheers
Bruce
On Mon, 15 Nov 2010, Ed Gronenschild wrote:
Hi,
Is there a tool to derive the cortical surface areas of
the cortical structures listed
Hi David,
I use both the MINC world and the freesurfer world.
One thing which may be of use to you or others, is to get from the
surface co-ordinates, back to world-coordinates (or scanner RAS), so
that minc tools etc. display things properly. To do this, you need to
apply a simple translation.
Rather than creating a subject in mni152 space, you can map your 152
data to our fsaverage (mni305) with
$FREESURFER_HOME/average/mni152.register.dat, eg
tkmedit fsaverage T1.mgz -overlay yourstats152.nii \
-overlay-reg $FREESURFER_HOME/average/mni152.register.dat
or
tksurfer fsaverage lh
Hi all,
I am new to Freesurfer and would like to generate a cortical (pial) surface of
1 subject's brain, but I need the surface in MNI 152 space (this is for display
purposes, so that I can overlay clusters already in MNI space). What is the
best way to accomplish this? I already have the
Hi all,
I am new to Freesurfer and would like to generate a cortical (pial) surface of
1 subject's brain, but I need the surface in MNI 152 space (this is for display
purposes, so that I can overlay clusters already in MNI space). What is the
best way to accomplish this? I already have the
tkmedit finds ever triangle that intersects the viewing plane then
computes the closed contour connecting them. Is that what you want?
Bruce
On Fri,
19 Oct 2007, XJ Kang wrote:
Hi,
I can get all the ponits of the cortical surface in ascii format. Anyway I
can plot the contour of the 3D
Hi,
I can get all the ponits of the cortical surface in ascii format. Anyway
I can plot the contour of the 3D surface on a plane? I tried to find all
the points in one plane, but the order is not along the contour line. I
can only plot the surface as dots, instead of lines in a 2D plane. I
Dear list,
Is there a paper or any documentation describing how freesurfer
tessellate and smooth cortical surfaces? In particular, does freesurfer
use any specific variety of marching cube isosurface algorithm? Regular
surface smoothing (like the Laplacian smoothing) may cause undesired
Hi Kai,
it was described in the Dale, et al. 1999 paper in NeuroImage, or maybe
part in
that and part in the 2nd part of it (Fischl et al., 1999 also NeuroImage).
They are both on our wiki (surfer.nmr.mgh.harvard.edu/fswiki). We don't use
marching cubes, but a custom tesselation algorithm.
yes, you can manually draw them in tksurfer, save them as a label file,
then specify the label with -l label file name to
mris_anatomical_stats.
cheers,
Bruce
On Wed, 19 Apr 2006, Goradia, Dhruman D wrote:
Hello All,
Is it possible to find ROI based cortical surface measures using
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