Yes, that looks right (assuming that cortisol is your first variable)
On 11/7/2023 3:49 PM, Laura Willers de Souza wrote:
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Hello FreeSurfer Developers,
Following the FSGD examples on the website, I built the following test:
Question: Is there an
Several things
- don't use --init-fsl. If you don't specify, then it will use
mri_coreg, which will work better. You can also try --init-header
- your movable scan appears to be t2 weighted, so use --t2 instead of --t1
- look at the cost file (or send it). It is hard to say what the cost
You can map the curvature from fsaverage to the individual (or reverse)
and then load both on the surface to see if they agree. I think that CVS
will/can save intermediate registrations, so you might check those to
see if the problem is cropping up at a particular step.
On 11/9/2023 8:18 AM,
ANTs denoising is not used by default. Ants N4 is used to crfeate nu.mgz
On 11/6/2023 11:46 AM, Alexopoulos, Dimitrios wrote:
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To which anatomical volume is ANTs denoising applied to for generating
the orig surface?
We do ANTS denoising to the input T1
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Hi Yujing,
thanks a lot for your reply. It worked perfectly. I used the following
command:
mri_surf2surf --sd --srcsubject fsaverage --trgsubject CON01
--hemi lh --sval-annot input_atlas.gii --tval output_atlas.gii
Maybe it would be good to give
You have to know the coordinate system of the matrix. See, eg, here
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
Once you know the coordinate system, I would use lta_convert to generate
an appropriate file, eg,
lta_convert --inlta identity.nofile --src preop.mgz --trg postop.mgz
Can you run it with --debug as the first option and send the resulting
terminal output?
On 11/9/2023 12:54 PM, Mirsol Choi wrote:
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Hello Freesurfers,
I am trying to segment the hippocampus into its subfields and take the
FA values from each subfield
Can you send
/data/Ghana_MRI_Data_lmid/StructT1/subjDir_FS_GHANA/Contrasts/GM_FM_ONE_minus_ZERO.mtx
?
How did you create this file? A lot of word processors will add special
characters that can cause a read failure.
On 11/9/2023 12:33 PM, Ludmila Midrigan wrote:
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Hello,
We are in the midst of longitudinal data collection. Before diving into our
first longitudinal structural processing, have a few questions:
Does Synthseg include a longitudinal processing stream?
If so, how does it compare to the Freesurfer
