Dear Douglas,
Thank you for your reply. Does this mean that if I were to have a
continuous variable (i.e. Neuroinflammation) and a categorical variable
with 2 levels (i.e. gene positive and gene negative), interaction can also
be found using QDEC?
Thank you.
Best Regards,
Heidi Foo
On Wed, Jan
Hi Bruce,
Thanks!
The -bigventricles flag worked like a charm! But I have now run into other
cases with fuzzy data and thin cortex that are not captured, such as the
picture below:
Any tips on filing them out?
Thank you.
On Sunday, April 23, 2017 3:41 PM, Bruce Fischl
wrote:
yes,
Hi Shane
I can't really tell from the image. YOu can try setting some of the
intensity bounds in mris_make_surfaces and mri_segment (eg. wlo, ghi and
such). If you upload the subject I'll take a look
cheers
Bruce
On Wed, 26 Apr 2017, Shane Schofield wrote:
Hi Bruce,
Thanks!
The -bigvent
Dear FS experts,
I’m trying to transform some files from fsaverage space to fsaverage5 space
using mri_surf2surf(FS version: 6.0), however, it is weird that the results
turn out to be all zeros on the fsaverage5 surface, the command line I used is :
mri_surf2surf –srcsubject fsaverage –sval ${h
I took a look at the xhemireg script and I feel like editing this to serve my
purposes might be too tall of an order.
However, I think I have a processing stream that will work — I want to make
sure there’s nothing problematic about it.
1. Run recon-all on the properly oriented T1 images throu
I just tried it, and there was not a problem. Are you sure that
hem.fsaverage.nii.gz has non-zeros in it? Can you send it to me? What
platform are you using?
On 04/26/2017 11:55 AM, dongnandi1 wrote:
>
> Dear FS experts,
>
> I’m trying to transform some files from fsaverage space to fsaverage5
In the mri_label2label command you have lh.aal.label as the input and
output. Are you overwriting the input and so now it does not match the
original subject?
On 04/25/2017 09:23 PM, haidong wang wrote:
> Hello FS experts,
> I want to get the thickness of 90 ROIs of AAL using freesurfer. I
Yes
On 04/26/2017 09:15 AM, Heidi Foo wrote:
> Dear Douglas,
>
> Thank you for your reply. Does this mean that if I were to have a
> continuous variable (i.e. Neuroinflammation) and a categorical
> variable with 2 levels (i.e. gene positive and gene negative),
> interaction can also be found u
Dear Freesurfer experts,
I would like to extract time courses of certain brain structures from the
stc file in Matlab. Could someone please let me know how I can determine
the lables of 10242 verices of my stc file? Or is there some matlab
function that gives the time course of a barin structure.
Any chance I could get some help on this? still having this problem
> On Apr 20, 2017, at 6:26 PM, Jared P Zimmerman
> wrote:
>
> Hi FS Experts,
>
> I’m having trouble getting anatomical stats from a parcellation I made out of
> scanner-space volume ROIs. I have taken the following steps to
Hi Jared
can you send us the full command line and screen output?
cheers
Bruce
On Wed, 26 Apr
2017, Jared P Zimmerman wrote:
Any chance I could get some help on this? still having this problem
On Apr 20, 2017, at 6:26 PM, Jared P Zimmerman
wrote:
Hi FS Experts,
I’m having tro
Hello FS experts,
I have a question regarding FS-Fast processing. I have performed
(successfully!) an FS-Fast single subject analysis. The results look fine
in the fsaverage space, but I'm interested in viewing them in the subject
space.
Are the registration files used along the processing pipel
Hi Patrycja
the standard transform we use to fsaverage coordinates is surface-based
(spherical). If you sample your EPI onto the surface, I believe you can
use mri_surf2surf to transfer it from subject to fsaverage
cheers
Bruce
On Wed, 26 Apr
2017, Patrycja Naumczyk wrote:
Hello FS expert
Hi Bruce,
thanks for a quick reply! mri_surf2surf worked fine just with specifying
the target and source subjects, no registration file needed - much
appreciated :)
Best regards,
Patrycja
2017-04-26 22:51 GMT+02:00 Bruce Fischl :
> Hi Patrycja
>
> the standard transform we use to fsaverage coor
glad it worked out :)
On Wed, 26 Apr 2017, Patrycja Naumczyk wrote:
Hi Bruce,
thanks for a quick reply! mri_surf2surf worked fine just with specifying the
target and source subjects, no registration file needed - much appreciated
:)
Best regards,
Patrycja
2017-04-26 22:51 GMT+02:00 Bruce Fisc
Hi Mailing List,
Still trying to solve the below medial surface problem. Does anyone have any
ideas?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1883 F +61
Great, thank you!
Regards,
Heidi Foo
On Thu, 27 Apr 2017 at 12:17 AM, Douglas N Greve
wrote:
> Yes
>
>
> On 04/26/2017 09:15 AM, Heidi Foo wrote:
> > Dear Douglas,
> >
> > Thank you for your reply. Does this mean that if I were to have a
> > continuous variable (i.e. Neuroinflammation) and a ca
Hello FreeSurfer experts,
I came across a paper:
http://www.sciencedirect.com/science/article/pii/S0166432815001837
where correlation maps between volume and gyrification are reported.
I am familiar with GLM in FreeSurfer i.e. correlating behavioral measures
with volume and gyrification but I was
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