Done
On 3/29/2024 3:31 PM, Aaron Tanenbaum wrote:
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I am currently running FreeSurfer 7.4. I wrote a script using the
program mri_volsynth. I noticed for the first time the program was
trying to write files where it did not have write permissions. It
what do you mean "extract" the cluster? Do you want mean thickness for
each cluster? Or the mean contrast? Of all the voxels in a cluster? For
the first two, you can use something like
mri_segstats --seg clusterseg.mgz --i contrast.mgz --sum summary.txt
On 3/26/2024 9:47 AM, Liliana Wu wrote:
What are the errors that you are facing? Can you provide more detail?
On 3/26/2024 9:12 AM, Saifullah Tumrani wrote:
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I am using freesurfer to preprocess my t1w 3d Mris using autorecon1
which includes first 5 preprocessing techniques till skullstripping it
Is that an MP2RAGE? The background may be messing things up. You can try
masking it, eg,
mri_synthstrip --i yourimage.mgz --o stripped.mgz
Then pass stripped.mgz to recon-all
On 3/25/2024 6:33 AM, Chen Yang wrote:
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>
> Dear FreeSurfer Developers,
>
> I am
That 2mm for the gaussian is just the post-processing filter and does
not represent the full amount of partial volume effect. What kind of
scanner is it?
On 3/22/2024 12:42 AM, WONG Wan Wa wrote:
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Hi Douglas,
Thanks for your clarification. This is my
oops, should have read your 2nd email. Yes, jacobian is the reason
On 3/20/2024 5:34 AM, tyzh...@ibp.ac.cn wrote:
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Dear FreeSurfer Experts,
Sorry, I think I've found the answer. It's because Jacobian correction
was performed for mris_preproc, right?
When working with area, you need to turn on jacobian correction.
mris_preproc will do this automatically, but you have to add --jac to
mri_surf2surf explicitly
On 3/20/2024 4:31 AM, tyzh...@ibp.ac.cn wrote:
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Dear FreeSurfer Experts,
I'm currently working
Oh, I see you are using 7.1.1. You can upgrade to 7.4.1. This will not
change the basic recon-all output and you'll have access to those new
features.
On 3/16/2024 4:21 PM, Stanica, Maria wrote:
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We checked and the ?h.orig surface looks right. We tried
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I am currently running FreeSurfer 7.4. I wrote a script using the program
mri_volsynth. I noticed for the first time the program was trying to write
files where it did not have write permissions. It outputted a few error
messages but gave a 0 exit
