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Hi Douglas,
Thanks for your reply!
I tried, but the volume and T1 still don't align.
my purpose:
make a mask of superior colliculus
Here is how I did:
1) tkregister2 --mov T1.nii --s sub01 --regheader --noedit --reg register.dat
2) open freeview an
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Hello Jessica,
please see my inline reponses below.
Best regards,
Kersten
On Mo, 2019-12-02 at 02:48 +, Hua, Jessica wrote:
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> Hi FreeSurfer Experts,
>
> I used the longitudinal pipeline and analyze
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Thanks Doug. we double checked the registration with gtm.seg.mgz and it
looks good. Also the uptake in Acc is not much smaller than other regions
and is pretty similar on both hemispheres so we are not sure what could be
causing this. Any suggestions mu
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Yes, absolutely, this should work! Many Thanks!
I have just one last question concerning the colors in FreeView.
I have a fsgd file with class 1 (patients) coming first and then class 0 (hc)
after.
The contrast matrix is 1 -1 0.
Among the results I see
Yes, that is the correct interpretation of the colors
On 12/3/2019 9:51 AM, Ferraro, Pilar wrote:
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>
> Yes, absolutely, this should work! Many Thanks!
> I have just one last question concerning the colors in FreeView.
> I have a fsgd file with class 1 (patien
Look at the lh.orig.nofix and see if you can find the defect. Also, look at it
in the volume and the surface views. Might be cerebellum
On 12/3/2019 11:30 AM, Laurel Quinlan wrote:
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Hi Freesurfer Support,
One of my colleagues receives the following error aft
it might also be the hemispheres not being separated, hard to tell
(although that almost never happens). You can look at the filled.mgz to
check this (the hemis should have different labels)
On Tue, 3 Dec 2019,
Greve, Douglas N.,Ph.D. wrote:
Look at the lh.orig.nofix and see if you can find t
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Dear Dr. Douglas,
Thank you so much for all the answers. I have two more questions.
1, When the Monte Carlo simulation is doing, how does one simulation is
done?
- synthesize z map (synthesize z map for how many subjects?)
- smooth z map (You
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Hi Freesurfer Support,
I'm wondering how ?h.surfaceholes prior to fixing and "Total number of defect
holes in surfaces prior to fixing" are calculated in the aseg.stats file for
each brain. I compared aseg.stats files for the same brain edited by two
Yes, looks like small registration errors. I don't think it is problematic. Any
vertex where even a single subject has a 0 should be masked out of the final
analysis.
On 12/3/2019 1:42 PM, Joëlle Ismay Rosanne Van Der Molen wrote:
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Hi Douglas,
Thank you for
On 12/3/2019 1:36 PM, Ting Li wrote:
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Dear Dr. Douglas,
Thank you so much for all the answers. I have two more questions.
1, When the Monte Carlo simulation is doing, how does one simulation is done?
* synthesize z map (synthesize z map for how many s
Those are the number of defects in the ?h.orig.nofix. Not sure why the two
people see different numbers. Are you totally sure they are being run in
exactly the same way? If they made different edits (control points, brain mask)
then it could result in different number of holes
On 12/3/2019 2:38
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Ok thanks a lot, that was helpful!
Best,
Joëlle
De : freesurfer-boun...@nmr.mgh.harvard.edu
de la part de Greve, Douglas N.,Ph.D.
Envoyé : mardi, 3 décembre 2019 21:09:34
À : freesurfer@nmr.mgh.harvard.edu
Objet
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Dear Dr. Douglas,
Thank you so much.
I have difficulty to understand z map is essentially an infinite # of
subjects.
Before smooth, there is no GLM analysis. Does the smooth include in the GLM
process?
Best regards,
Ting
On Tue, Dec 3, 2019 at 2:14
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