1. You are better off expanding the white surface by 3mm using
mris_expand.
2. There is code around for this but I don't know it, perhaps Matti
and/or Rudolph can comment.
3. What are you merging?
cheers
Bruce
On Tue, 7 Jan 2014, Octavian Lie wrote:
> Dear All,
>
> 1. I need to erode the ?h.p
Thank you,
I want to merge the pial eroded (of white expanded) and downsampled
surfaces of the two hemispheres in a new surface (generate a new,
continuous, surface/mesh, no holes, no self intersections). The
question is
whether pial freesurfer atlases and spherical registration would be
applica
Thank you Martin.
I will try this approach. I was able to temporarily move the longitudinal
subject data to its own folder to run aparc2table and aseg2table. Hopefully
this will also work for the hippocampal subfield script.
Best wishes,
Sal
Salil Soman, MD, MS
Postdoctoral Research Fellow - S
Dear Free Surfers,
I have a short question regarding the mapping of vertices of the fsaverage_sym,
how do vertices in the left hemisphere correspond to vertices in the right
hemisphere?
When I tested it, it did not seem that the first-indexed vertex on the left
hemisphere corresponded to the
Hi Sal,
asegstats2table (and aparc..) will take the longitudinal qdec file and
then automatically select the *.long.* directories to create the table.
So there is no need to move them to a separate folder.
The longitudinal qdec file is simply a table with at least 2 columns
(for stacking res
Dear All
I reoriented a volume on exporting to analyze format for an application
mri_convert -i path to file/T1.mgz --out_orientation PSR -o path to
file/T1reoriented.mgz
mri_convert -ot analyze -i path to file/T1reoriented.mgz -o path to
file/T1reorientedPSR.img
I need to reorient from the com
can't you just use the existing spherical registration? Each subject has
already been registered, so if you can keep track of the correspondence
between downsampled and full surfaces you should be able to use the
existing registration
On Wed, 8 Jan 2014,
Octavian Lie wrote:
> Thank you,
>
> I
Hi Sofie,
no, they don't correspond. You need to use mri_surf2surf to map one to
the other (which is a bit tricky).
cheers
Bruce
On Wed, 8 Jan 2014, Sofie Valk wrote:
> Dear Free Surfers,
>
> I have a short question regarding the mapping of vertices of the
> fsaverage_sym, how do vertices in t
To follow up, it is intended that you will map both hemispheres of a
given subject to one of the hemispheres of fsaverage_sym (it does not
matter which, but we usually use lh). You can then do the comparisons on
that hemisphere. Does that make sense?
doug
On 01/08/2014 02:09 PM, Bruce Fischl
Thanks Bruce! How long would it take to build an atlas?
What are your thoughts Mike?
On 7 January 2014 14:38, Bruce Fischl wrote:
> Hi Linda
>
> I actually don't know the ethnicity of the subjects in our atlas. I wouldn't
> expect it to be an issue for folding patterns, but it is possible. You
Hi Linda
I had an old address for Mike in the first email. I think this one is
correct. Building a folding atlas is pretty quick, depending on how many
subjects you have. You'll need to pick one subject, run mris_make_template
to build a single-subject template (for each hemi), register everyon
Dear Freesurfer experts,
I have a question about cortical thickness analysis using freesurfer. Since
I don't know how to post my question in freesurfer mailing list, that is
why I am writing to you to get some help. Hopefully, my email will not
cause you any troubles.
My question is : When I com
On 01/08/2014 04:28 PM, yaya ya wrote:
> Dear Freesurfer experts,
>
> I have a question about cortical thickness analysis using freesurfer.
> Since I don't know how to post my question in freesurfer mailing
> list, that is why I am writing to you to get some help. Hopefully, my
> email will no
what was your mri_label2vol command and terminal output?
doug
On 01/06/2014 02:35 AM, Frank Hsieh wrote:
> Dear FreeSurfer Users,
>
> I ran recon -all on my structural image and created ROI masks (using
> mri_label2vol) based on FreeSurfer's cortical parcellation. I'd like
> to use these masks f
Does the same thing happen in freeview?
On 01/06/2014 04:45 AM, L. Schweren wrote:
>
> Dear experts,
>
> I ran recon-all with qcache. When loading the right hemisphere of
> fsaverage (or any other surface reconstruction) into tksurfer (for
> example command: tksurfer fsaverage rh white), the
yes, use scale brain. For talairach registration it is ok (not for
within-subject registration). I don't know why this happens
doug
On 01/06/2014 12:21 PM, Bruce Fischl wrote:
> it probably doesn't matter, but Doug is the Talairach expert, so
> perhaps he can comment
> Bruce
>
> On Mon, 6 Jan 2
You can do it to the sig file (the p-value already assumes a two-sided
test). Why do you want to do it with the ces and cesvar files? If you
are planning to use the abs(ces) for a higher level analysis then you
need to be very careful as you can get some unintended effects
doug
On 01/07/201
Several potential problems. It makes the statistics non-gaussian and the
abs(ces) becomes noise dependent (and so there will be a noise dependent
bias). This makes interpretation more difficult (eg, is a difference
between groups a difference in ces or a difference in noise?). The
non-gaussian
Hi Doug,
Can u help ?
Thanks
Rotem
Rotem Saar-Ashkenazy
Department of Brain and Cognitive Science
Ben Gurion University of the Negev
Beer-Sheva 84105
Israel
2014/1/6 Bruce Fischl
> it probably doesn't matter, but Doug is the Talairach expert, so perhaps
> he can comment
> Bruce
>
>
> On Mon,
Hi everyone,
I have a question related to Monte Carlo tests of multiple comparisons. When I
conduct some of my analyses, there is no difference between before and after
Monte Carlo (i.e. same size and coloured regions appear on the inflated brain
after I click on the analysis in the Description
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