not sure what is happening. You can run recon-all with -debug and
capture the output (both stdout and stderr) into a file. This will cause
it to print out huge amounts of text specifying what it is doing on each
line. You should also see if there is some stderr output that is not
being caught.
Sorry, I don't know what you mean by enorm threshold. Can you elaborate?
On 4/4/2024 4:39 PM, Sneha Pandya wrote:
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Dear team,
I am using mc-afni2 to perform motion correction on dynamic PET images
(ref: petsurfer wiki page). I am planning to use an
On 4/18/2024 1:59 PM, Tejaswi D. Sudhakar wrote:
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Hello Freesurfer team,
I am interested in doing one glm analysis using both the thickness and
cortical surface area.
My question is two-fold:
First, is it possible to provide both the thickness and
thanks, just checked in your change.
On 4/17/2024 9:37 PM, Tyler Slouf wrote:
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Hello FreeSurfer Developers,
I found what I believe to be a bug. Typically I can load mgz files
into my Matlab program without any trouble.
But if the path containing the mgz
You can try running samseg. This will generate most of the layers you
want, but in segmentations. You will have to convert them to surfaces
(eg, mri_tesssellate or mri_binarize with --surf output)
On 4/15/2024 5:31 AM, XIE Jing wrote:
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Hello all,
We
Yes, you can also run
mris_fwhm --smooth-only --i input.surf-values.mgz --fwhm FWHM --s
subject --hemi hemi --o output.surf-values-smoothed.mgz --cortex
This will give the same result as mri_surf2surf
On 4/12/2024 10:07 PM, Jiaen Liu wrote:
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I found in
The vsm (voxel shift map) needs to be in the same voxel space as the
fMRI (ie, it has to have the same voxel size, number of voxels, and the
voxels must line up with the fMRI)
On 4/11/2024 8:11 PM, Gianluca Guglietti wrote:
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Hi,
I had a question as to
Hi Knut,
Can you clarify what you mean by your question?
Lilla
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Knut J Bjuland
Sent: Friday, April 5, 2024 2:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] question about infantfreesurfer
Hi Sanna
They were kind of hand tuned ages ago, but I'm pretty sure that they get
re-estimated by a procedure that adapts to the intensities in the input images.
They were probably tuned for a specific class of T1-weighted scans (like
FLASH), but the adaptive estimation usually works well on a
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Hello Freesurfer team,
I am interested in doing one glm analysis using both the thickness and cortical
surface area.
My question is two-fold:
First, is it possible to provide both the thickness and area files to
mris_preproc and mri_surf2surf
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Dear FreeSurfer developers,
I am interested in understanding where the freesurfer default intensity values
for gray and white matter specifically come from within the recon-all command.
I understand the default intensity of white matter (mean) is
vertices require a surface. There is no surface for cerebellum, so the
vertices are all marked -1 to indicate that the vertex indices are not
valid. The XYZ values are valid though
On 4/9/2024 6:36 AM, Sam W wrote:
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Hello!
I'm trying to convert the
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