Try renaming the reg to something.lta
On 12/10/2019 11:04 AM, Vicky Yang wrote:
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Dear Freesurfer experts,
I am using bbregister to register my functional template image into T1 image.
The bbregister is running fine. But when I tried to view registration usin
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Hi Kersten,
Thank you for all of your help so far. I have now located the unstandardized
beta values in lhstats(i).Bhat. Unfortunately one of the effects I was
interested in was the slope for years within my case group, which required the
use of th
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That's what I needed, thanks! It all worked well now.
Actually using '--conform_min' preserved existing image dimensions as
desired, otherwise image got reshaped to 256^3 raising the aforementioned
dimensionality error.
Jordi
On Thu, Dec 5, 2019, 18:
External Email - Use Caution Hi there, I obtained results for right thickness using aparcstats2table.Then, ANCOVA was used to compared right thickness between two group (age, sex, edu, ICV as covariates)using SPSS. AA group showed higher right thickness in the superior frontal gyrus
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That sounds good to me! The file is about 100MB so I got a sharing link
here.
https://drive.google.com/file/d/15IfN6EzZj_wAW1y0v8USIs2tthfpdH95/view?usp=sharing
On Tue, Dec 10, 2019 at 12:46 PM Bruce Fischl
wrote:
> the topology fixing output should
the topology fixing output should let you find the defect that is so big
and figure out how to fix it. If you want to tar/gzip the entire subject
dir and send it to us we will be happy to help
cheers
Bruce
On Tue, 10 Dec 2019, Kong
Chuizheng wrote:
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yes. It is hard to predict the effects of tumors on the topology of the
surface. It might be fine or it might need fixing. And I expect the program
isn't actually frozen. The time to fix a defect is quadratic in the number
of vertices in the (convex hull) of the defect, so for small ones it is
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I was looking at this page
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview)
on finding and fixing holes using wm.mgz. I thought that tumor might not be
the primary reason that the program froze. I did have some subjec
have you looked at our tutorial on topology fixing? I would try that
first. You might need to fill in the tumor in the wm.mgz. The little holes
won't be a problem - it is the big ones that might be
cheers
Bruce
On Tue, 10 Dec
2019, Kong Chuizheng wrote:
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Dear Freesurfer experts,
I am using bbregister to register my functional template image into T1
image. The bbregister is running fine. But when I tried to view
registration using tkregisterfv, the window opened and closed quickly with
an error message:
Does your 3D model need to be topologically correct? What are you trying
to achieve? And are the holes/handles due to the tumor? Can you send us
some images?
cheers
Bruce
On Tue, 10 Dec 2019, Kong Chuizheng wrote:
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Hello Freesurfer Developers,
Hi Fredrik
yes, the subcortical segmentation can still be ok when the cortical
stream results are not that good
cheers
Bruce
On Tue, 10 Dec 2019, Fredrik wrote:
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Hi FreeSurfer experts,
In our data, we have a sample of older people with brain
Hi Zhang
look at the docs for mri_vol2surf. In particular, check out the various
--proj* options like projfrac and projdist
cheers
Bruce
On Tue, 10 Dec 2019, a Chinese
reader wrote:
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Dear Freesurfer experts,
I have some questions about intensit
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Hello Freesurfer Developers,
We are trying to construct a 3D cortex model of a tumour subject. The
recon-all.log showed that the program froze at Correction of the Topology with
"XL defect detected." I followed the procedure of the online tutorial
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Hi FreeSurfer experts,
In our data, we have a sample of older people with brain athrophy. This
influences the cortical segmentation, where it can take into consideratin the
skull, and/or leave out grey matter.
My question regards the subcortical se
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