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Hello,
I was wondering if there were any updates on this question?
Thank you,
Catherine
-- Forwarded message -
From: Catherine Tallman
Date: Thu, Nov 19, 2020 at 8:57 AM
Subject: Issue with custom label
To: Freesurfer support list
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Yes, what should I do if there is something wrong
-原始邮件-
发件人:"Greve, Douglas N.,Ph.D."
发送时间:2020-11-30 01:22:22 (星期一)
收件人: "freesurfer@nmr.mgh.harvard.edu"
抄送:
主题: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for
ev
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I think so.
Matt.
From: on behalf of Darko Komnenić
Reply-To: Freesurfer support list
Date: Monday, November 30, 2020 at 6:23 PM
To: freesurfer
Subject: Re: [Freesurfer] arguments to use after pial edits
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Than
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Thanks Matt!
Should I also add the -autorecon3 flag, or does that get performed
automatically if I put in "autorecon2"?
Best,
Darko
> Message: 4
> Date: Mon, 30 Nov 2020 19:16:06 +
> From: "Glasser, Matthew"
> Subject: Re: [Freesurfer] arguments
Hi Yezhe
It depends a lot on what your resolution, read out direction, bandwidth and
field strength are. We generally fix these with T2 or FLASH scans at the same
resolution/geometry/readout as the T1. Otherwise they are pretty tough as the
dura is close enough to the gray matter that you can’t
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I find the recon-all table to be helpful:
http://secure-web.cisco.com/1rQT1vL5GWrATp5z0Ct2LBj8MsEx75qijDiNOIOc1xsGTqc0VC-s7rH5tRIiUV_kHXR7CsV_-uoWR6y_oPuNxiCAZCmbkgfSfUxHd4oB4gX7XvLCt40MlQR_Ejq0tpN0lnJJt1uO1jl_1XWYZQv92-3NGME0PKZPC51_qjOKHk9cLfcojjN-As
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Dear Freesurfer experts,
I am using Human Connectone Project pipelines to calculate cortical myelin
levels. These pipelines use Freesurfer 6.
Since certain subjects' brain surfaces had some chunks and spikes sticking
out, I edited the brainmask.mgz file
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Hello VIttal,
thanks for the info about the design.
You wrote before that the Matlab variable X (i.e., the design matrix) has a
dimension of 47x6. X is a translation of the study design into a numerical
matrix, which is part of the statistical model
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Dear all,
The NIMH/NIH is looking for a skilled Octave/MATLAB programmer, with
knowledge of multivariate statistics, to implement inference for canonical
correlation analysis (CCA) using permutations, as described in the recent
paper
(https://secure-w
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Then, now that I have the AAL in the surface I should make a label for
every region in the AAL_surface image with mri_vol2label with surf option
and run mri_label2label for every label and every subject in my study. Is
this the correct workflow?
El lun
good question. I don't think there is anything wrong with multiplying two zs,
but it might be more appropriate to multiply the raw covariates and then
compute a z from that.
On 11/30/2020 4:07 AM, Marina Fernández wrote:
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Dear all,
I am doing a multiple reg
Oh, don't use .img as it cannot handle the surface dimensions. Technically,
nifti cannot either, but I hacked our nifti version to accommodate. Or use mgh
as you have done.
On 11/30/2020 8:31 AM, Alberto Del Cerro Leon wrote:
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First of all, thanks you Dougla
How was lh.sphere.reg created? It might be corrupted, so try creating it again.
On 11/30/2020 3:11 AM, 1248742467 wrote:
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Hello,Fs
When I used mri_surf2surf command to template the lh.thickness to fsaverage5
space, the error appeared:
Command:
mri_surf2surf -
what space is the vtk surface in?
On 11/30/2020 2:55 AM, 1248742467 wrote:
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Hello, what command can map VTK file to fsaverage5 space? I want its vertex
number to be 10242. If you know, please give me an example.
Looking forward to your reply
_
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First of all, thanks you Douglas for the support.
As I said i run the mri_vol2surf and I obtained an error:
mri_vol2surf --src /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI
--projfrac 0.5 --hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh
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Hello FS experts
Thank you for your kind response.
This is regarding my previous mail.
I think we need to talk about the design matrix X first (sorry, I did not
look at your xlsx file; I think it's probably better to send simple csv
files if at all).
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No problem, thanks!
So I shall send an email only to freesurfer or would it fine if I put you
in cc?
With regards
Vittal
On Mon, Nov 30, 2020 at 4:25 PM Diers, Kersten /DZNE
wrote:
> Hi Vittal,
>
> Sorry, I can only help on the public freesurfer l
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Hello Knut,
difficult question, since the output looks OK at first sight. Am I correct in
assuming that what you’ve posted is the complete output of that script, and
that the corresponding output is considerably longer when you run it on the
MacBook
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Dear all,
I am doing a multiple regression analysis with 3 covariates of interest. I
know that for testing two-way and three-way interactions I must create new
variables by multiplying the covariates of interest. As Freesurfer
transforms continuous var
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Hello, Fs
Do you know how to convert the .vtk to .annot file?
I want to visualization with. Annot file by freeview.
Looking forward to your reply!___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
h
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Hello,Fs
When I used mri_surf2surf command to template the lh.thickness to fsaverage5
space, the error appeared:
Command:
mri_surf2surf --srcsubject OASIS-TRT-20-1 --sval thickness --src_type curv
--trgsubject fsaverage5 --trgsurfval
/home/tj/applica
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