mris_expand
> On Aug 13, 2014, at 8:57 PM, Douglas N Greve
> wrote:
>
>
> You need a program whose name I can't remember. Bruce, what is the name
> of the program to create a surface midway between white and pial?
>
> Don, you can use this to create the mid surface (or project it to any
> d
yep, that's it
On 08/13/2014 03:08 PM, Markus Gschwind wrote:
> Hi!
>
> You probably mean
>
> mris_expand
>
> which creates a surf inside or outside of white, e.g.
>
> mris_expand surf/lh.white -1 surf/lh.white_1mm_inside
> # use positive values for outside ?h.white border
>
> mris_expand -thickne
Hi FreeSurfers,
I have gone through correcting pial surfaces for one subject, and ran the
script to regenerate the surfaces:
recon-all -autorecon-pial -subjid 1
After running without error, it appears the pial surfaces have not changed at
all. Does FS overwrite the previous lh.pial and rh.pial
Fantastic - thank you.
Don
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwi
Hi!
You probably mean
mris_expand
which creates a surf inside or outside of white, e.g.
mris_expand surf/lh.white -1 surf/lh.white_1mm_inside
# use positive values for outside ?h.white border
mris_expand -thickness surf/lh.white -1 surf/lh.white_in100%_thickness
# this samples in % of GM thick
You need a program whose name I can't remember. Bruce, what is the name
of the program to create a surface midway between white and pial?
Don, you can use this to create the mid surface (or project it to any
depth) and to create a surface that is just inside the WM (use a
negative projection d
Thanks for posting back so quickly and for the clarifications.
What I am looking for is a list of vectors which are in the gray matter and a
2nd list that are inside the nearby white matter.
It sounds like the "white" are inside the white matter but near the boundary
with the gray.
Is it reasona
On 08/13/2014 02:11 PM, Krieger, Donald N. wrote:
>
> mri_annotation2label enables extraction of vectors from .annot files
> to .label files, one file per label.
>
> One may choose orig, white, or pial vectors.
>
> (1)orig vectors are on the cortical surface. The gray scale value for
> each of t
mri_annotation2label enables extraction of vectors from .annot files to .label
files, one file per label.
One may choose orig, white, or pial vectors.
(1)orig vectors are on the cortical surface. The gray scale value for
each of these is that of gray matter, correct? And these are inside
You can inflate it more with something like
mris_inflate -dist .01 -f .001 -no-save-sulc 20 lh.smoothwm lh.inflated
20 is the number of iterations (default is 15) so play with that number
On 08/13/2014 11:25 AM, angela.fav...@unipd.it wrote:
> Hi Doug,
> a further question: my final symmetric
Hi Doug,
a further question: my final symmetric atlas seems to be not inflated
enough, but still have important sulcations.
Do I have to perform further iterations (myatlas.i4, myatlas.i5 )
until the resulting volume is good enough? Or which is the correct method
(other than performing asymmetr
Thanks.
Regards,
Don
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas
If you use a different target, then it will not overwrite the output of
previous runs but names the files differently based on the new target
name. In the qdec interface, you should change the name of the
"Common-space Subject"
doug
On 08/13/2014 10:12 AM, Vy Dinh wrote:
> Dear developers,
>
use mri_convert with the --ascii flag
--ascii
save output as ascii. This will be a data file with a single
column of data. The fastest dimension will be col, then
row,then slice, then frame.
On 08/13/2014 10:11 AM, Krieger, Donald N. wrote:
>
> I just want print the list of vertices with their c
I just want print the list of vertices with their contrast percentages into an
ascii file.
Regards,
Don
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Wednesday, August 13, 2014 10:09 AM
To: freesurfer@nmr.mgh.harva
Dear developers,
I just have a brief technical question about using qcache for multiple
fsaverages. If I wanted to write my subjects to a new fsaverages, I know
that one can use the command
Recon-all -qcache -target fsaverage2 -s subid
However, does this overwrite the current normalized data to
I guess I don't understand what it is you want exactly. the gray/white
contrast file is in the surf folder. Do you want to compute a mean over
a given set of vertices?
On 8/13/14 10:06 AM, Krieger, Donald N. wrote:
Here is a fragment of the help text for recon-all which pointed me
towards
Here is a fragment of the help text for recon-all which pointed me towards this:
WM/GM Contrast (-pctsurfcon)
Computes the vertex-by-vertex percent contrast between white and gray matter.
The computation is:
100*(W-G)
pct = -
0.5*(W+G)
The white matter is sampled 1m
On 8/8/14 10:40 AM, Lars M. Rimol wrote:
Thanks, Doug!
So I tried this method using fsaverage/surf/lh.white.avg.area.mgh. The
results seem to be reasonably consistent with the ones I get when
eyeballing the p-maps overlayed on fsaverage in tksurfer. Would you
agree that's a reasonable "sani
What do you mean by contrast vectors?
On 8/13/14 9:36 AM, Krieger, Donald N. wrote:
What is the tool to extract the contrast vectors from surf/[
lr]h.w-g.pct.mgh ?
Thanks,
Don
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What is the tool to extract the contrast vectors from surf/[ lr]h.w-g.pct.mgh ?
Thanks,
Don
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The information in this e-mail is inte
oh, I see. Usually it's pretty good there. Sometimes if there is enough
motion, or lower res scans it can be hard to distinguish left from right
gray matter, but otherwise it is a pretty reliable set of regions I believe
cheers
Bruce
On Wed, 13 Aug 2014, amirhossein manzouri wrote:
Dear Bru
Dear Bruce,
I meant cingulate cortex, the cuneus and precuneus !
Best regards,
Amirhossein Manzouri
On Mon, Aug 11, 2014 at 12:53 PM, Bruce Fischl
wrote:
> Hi Amirhossein
>
> which structures do you mean? Like the ventricles? We usually mask those
> regions out using the ?h.cortex.label.
Hi Krista
I'm not sure we can. Certainly there are studies showing that in
congenitally blind populations V1 can get recruited for other things
cheers
Bruce
On Mon,
11 Aug 2014, krista kelly wrote:
> Just wanted to pose this question again to the Freesurfer community:
> Can anyone provide any
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