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
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?
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
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
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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
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