Dear Freesurfer experts,
I very much appreciate your help with an additional set of questions. I
feel I'm really close to getting this finished :)
1) In a design with group and gender as discrete factors and age as a
continuous factor, why is it that QDEC only displays the contrast Does the
avg
Hi Bruce,
Thanks for the quick response. The label is a manually traced area of the
cortex. It is in subject scanner space and has a single value, so it
probably would not work with bbregister. I can load it in tkmedit as a
segmentation and the alignment is correct. I attached a screenshot. Is
Hi Jonathan
you don't need to register it if it's shown properly in tkmedit or
freeview. Can you tell us more about what you are trying to do?
Bruce
On Sun, 12 May 2013, Jonathan DuBois wrote:
Hi Bruce,
Thanks for the quick response. The label is a manually traced area of the
cortex. It
Hi Bruce,
I would like to convert the .mgz label volume to a surface label for that
subject, but mri_vol2surf requires a registration file.
Best,
Jonathan
On Sunday, May 12, 2013, Bruce Fischl wrote:
Hi Jonathan
you don't need to register it if it's shown properly in tkmedit or
freeview.
try using --regheader
cheers
Bruce
On Sun, 12 May 2013, Jonathan DuBois wrote:
Hi Bruce,
I would like to convert the .mgz label volume to a surface label for that
subject, but mri_vol2surf requires a registration file.
Best,
Jonathan
On Sunday, May 12, 2013, Bruce Fischl wrote:
Hi
Hi everyone,
We are trying to restrict an analysis using Qdec to a region of interest. We
have successfully created the ROI mask, however the analysis continues to be
run on the entire brain. Any help is greatly appreciated.
Thanks,
Skyler and Jon
--
Skyler G. Shollenbarger
Graduate
I used the following options: mri_vol2surf --hemi lh --regheader subject01
--cortex --mov label.mgz --o ./label.mgh
It ran without error, but I could not open the resulting file in tksurfer
as either a label or an overlay:
-
/Applications/freesurfer/tktools/tksurfer.bin: no data in label
This is available online now:
http://authors.elsevier.com/sd/article/S1053811913005053
On 5/7/13 3:10 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
actually Matt Glasser points out that a brief description is in his paper
that is coming out soon, and there is also some description in
Hi Panagiotis,
On 5/12/13 9:32 PM, Fotiadis, Panagiotis wrote:
Hi Freesurfer experts,
I was wondering about three things concerning the use of the mri_glmfit-sim
command:
1) I tried running it with the --2spaces flag in order to Bonferroni correct
over the two hemispheres but it tells me
Hi Skyler, I don't think we have the ability to restrict the analysis to
an ROI in QDEC. You can do it with mri_glmfit with the --mask or --label
option.
doug
On 5/12/13 4:25 PM, Skyler Gabriel Shollenbarger wrote:
Hi everyone,
We are trying to restrict an analysis using Qdec to a region of
It cannot create a label file directly. What happens when you try to
load it as an overlay? Make sure to set the threshold to 0.5. Also,
before going to the surface load the binary volume onto the anatomical
with the surfaces to make sure that the surfaces pass through the mask.
doug
On
On 5/11/13 7:41 PM, Tudor Popescu wrote:
Hi everyone, I resort to asking some questions here again, after
feeling increasingly stupid (maybe just tired) after reading the wiki
pages relevant for my analysis (ROI, thickness).
1) How should the contrast vector for a group comparison while
Hi Xi-Nian, it does not do the same thing, but it does something
similar. Anderson found that it gave similar results in a lot of cases,
but he has found some differences. If he's still following the FS list,
maybe he can comment.
doug
On 5/11/13 9:53 PM, Xinian Zuo wrote:
Hello Doug,
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