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Hi,
I am just writing to ask whether you have time to look into the maillist
redirecting issue? It would be very helpful to be able to read the existing
questions in the maillist. Are there any other ways to search and access
the previous QnA emails? T
yes, the vertices in one subject do not have any correspondence to vertices in
an other subject
On 10/25/19 12:08 PM, Nasiriavanaki, Zahra wrote:
Hi Freesurfer experts
I have a few labels that correspond to activation clusters in fsaverage space
for an individual subject. I used mri_label2label
Hi Doug
Thanks for your reply.
Could you pleas let me know how I can solve this issue?
How should I view those labels on the subject’s native space?
Thanks
Mona
On Oct 28, 2019, at 10:18 AM, Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
yes, the vertices in one subject do not
Yes, this is the issue we have with the high res stream in v6. As I said, you
can use the patch that I pointed to below to get better surfaces.
On 10/25/19 12:30 PM, Alexopoulos, Dimitrios wrote:
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Opps, here are the snapshots. The aseg subcortical look good u
12 DOF is probably not going to help much. I vaguely remember that there were
some tools out there that would attempt to fit the non-linear parts of the B0
map. Maybe in fmriprep? Sorry, can't give you more guidance than that.
On 10/26/19 10:56 AM, Daniel Callow wrote:
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what is your request?
On 10/26/19 1:20 PM, Larry Lai wrote:
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Hello FreeSurfer Users
I'm attempting to explore the correlations between the surface-based and
voxel-based values and adjusted for nuisance covariate in FreeSurfer.
Correlational study:
A. Cortic
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If I get the question correctly, all you have to do is:
1) not run mri_label2label at all
2) replace 'fsaverage' with the subject identifier in the command, e.g.:
tksurfer subject23 lh inflated -ov sig.nii.gz
Best,
Tim
> On October 28, 2019
Which version of FS are you using? One thing you can try is
setenv LANG en_US.UTF-8
or if you on bash
export LANG=en_US.UTF-8
On 10/26/19 2:56 PM, Renew Andrade wrote:
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I don’t know what do you mean by not knowing what it means. I said that I have
tried all
My guess is that your covariates have almost no range to them and so look like
constant (similar to columns 1 and 2). You can try demeaning and rescaling the
covariates. You can do this by hand and create a new FSGD file or you can add
the following lines anywhere in the fsgd:
RescaleFlag 1
Deme
Did you run recon-all from the beginning? It needs to create those files
On 10/27/19 3:18 PM, Adam Rytina wrote:
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Hello all,
I´m struggling with running "recon-all -skullstrip", in general with
"recon-all". I added NIfTI series file to a new directory "QWE"
Hi Tim
Thanks for you reply.
I did use the command you recommended ( tksurfer subject23 lh inflated -ov
sig.nii.gz )
But, I don't see any activation on it. However, when I use ( tksurfer
fsaverage lh inflated -ov sig.nii.gz ), I see patches of activation.
Is it because my whole analysis
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Thanx Doug.
Tried the patch and got similar results to -hires. Must be the data and tissue
contrast in that region where WM is difficult to discern.
These are 2yo subjects. We also tried baby freesurfer with poorer results.
Jim
From: freesurfer-bo
Hi Andrade,
This probably has to do with SIP being enabled, which blocks libraries stored
in /usr. I would suggest disabling SIP and rerunning to see if that fixes
things:
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/
best,
Andrew
___
Hi Rachel, the mailing list archives are available to search through at
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Rachel S
Sent: Monday, October 28, 2019 10:08 A
Am I correct in assuming this results in z-scoring/normalizing the covariates?
Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging
> On Oct 28, 2019, at 7:33 AM, Greve, Douglas N.,Ph.D.
> wrote:
>
> My guess is tha
Yes
On 10/28/19 1:04 PM, Nillo, Ryan Michael R wrote:
> Am I correct in assuming this results in z-scoring/normalizing the
> covariates?
>
> Ryan Michael Nillo
> Staff Research Associate I
> University of California San Francisco
> Department of Radiology and Biomedical Imaging
>
>> On Oct 28, 20
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Thanks, Doug. One more question: I want to see how correlated my covariate ROI
is with LGI and compare the correlation maps between the two groups. Is my
glmfit command the correct setup? I have tried running glmfit on a different
fsgd and contrast m
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Hello,
what do you mean by the beginning? You mean to download the tutorial set and
run recon-all on that?
Thanks
Adam
Od: freesurfer-boun...@nmr.mgh.harvard.edu
za uživatele Greve, Douglas N.,Ph.D.
Odesláno: pond
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Dear experts,
In the context of the BIDS transforms extension and the ".x5" format we
chatted about in the workshop we made in March at MIT, we are addressing
the following question.
We have a sphere of fsLR coordinates in fsaverage space (e.g.,
https
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From: Timothy Coalson
Reply-To: Timothy Coalson
Date: Monday, October 28, 2019 at 8:21 PM
To: "Glasser, Matthew"
Subject: Re: FW: [Freesurfer] Mapping coordinates from sphere file to ?h.white
That is not a sphere of fs_LR coordinates (in fact, "fs
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Hi Kersten,
Did you recieve the files I dropped to [ mailto:mreu...@nmr.mgh.harvard.edu |
mreu...@nmr.mgh.harvard.edu ] on the 16th of October (titled
'BAR_Sydney_FSIssues_SurfThreshLabels.zip')?
Kind regards,
Bronwyn Overs
Research Ass
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