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To Freesurfer team,
Hi everyone, sorry for bothering. I am looking for correlation analysis
in a cohort of subject between cortical thickness and an external score
(and corrected for age). Because I am only working on one group (with 2
covariates),
Good morning Freesurfers!
I am building a GLM with 4 classes (control_F, control_M, patient_F, patient_M)
to check for differences in cortical thickness between patients and control
accounting for the effect of gender and age on cortical thickness.
How should my contrast be?
Thanks a lot,
Val
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Dear all,
I want to process brains with tumor lesions with the recon-all -all command.
Recon-all (freesurfer version 6) gets always stucked when calling the function
mris_fix_topology. It used to work with freesurfer version 4.5, but I still
want to
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Yes, the lh.orig is changing, but not lh.white. (I responded to this on the
23rd, but the reply didn't show up in the archive and I'm not sure it went
through, so I'm trying again.) Thanks,
Ben
On Wed, Dec 23, 2020 at 12:37 PM Greve, Douglas N.,Ph.D.
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Let me rephrase:
I am running an analysis with two groups, a patient group (n=23) and a healthy
control group (n=24). I have accomplished 3DT1 recons for all participants. Now
I want to correct pial surface using 3D Flair images.
However, I have dif
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Dear All,
These are probably rookie questions.
1. I can read an .annot file with read_annotation.m, is there a way to
write one? (for example read it to matlab, modify, and save, or create a
combined (lh+rh) aparc.annot file etc.
2. On the same line,
Hi Octavian
1. Yes, there is a write_annotation.m that you can use.
2. We output an annot of the max probability labels at each point I think
called BA_exvivo.thresh.annot
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Octavian Lie
Sent: Friday, January 8, 2021
Alas there is not – there are large parts of the cortex that have not yet been
mapped for microstructural boundaries
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Octavian Lie
Sent: Friday, January 8, 2021 11:59 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] write .annot
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Thank you, Bruce. Just to exhaust the annot issue. I assume that the labels
(parcel names) are not embedded in .annot or aparc+aseg.mgz per se, but
they are read from the LUT table by matching annot vertex indices to col 1
in the LUT. Is there any .m fi
Hi Octavian
Yes, we do usually embed the LUTs into the .annot and .mgz files to make them
self-contained. I think Doug has something to read them from at least the .mgz.
Maybe mri_info?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Octavian Lie
Sent: Friday, January
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You can always give it a try and put slice thickness as a covariate of no
interest.
Matt.
From: on behalf of Georgia Kapizioni
Reply-To: Freesurfer support list
Date: Friday, January 8, 2021 at 10:22 AM
To: "freesurfer@nmr.mgh.harvard.edu"
Subje
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