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Hi Bruce,
thank you very much for taking a look at that. I uploaded 3 images in
different orientations. I can not see any white matter.
Cheers
Carolin
On Fri, Mar 19, 2021 at 7:26 AM Fischl, Bruce
wrote:
> Hi Carolin
>
>
>
> Yes, I guess send
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Thx Doug.
I as clarifying because I thought I read earlier that the -hires option will
downsample the surface to a number of vertices equal to the number that would
have resulted if recon-all had been run at 1mm. Is this not different from
Hi Ursula,
Thanks for pointing this out. I think it’s just the case that MCR wasn’t
installed in that container. I’m surprised this hasn’t been brought up before.
We’ll update the container with it.
best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Ursula Tooley
Date:
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Hi Freesurfer experts,
I’m trying to use the official FS 6.0.0 container from Dockerhub on a new HPC
(for consistency with previous pipelines), and got the error below about not
finding the Matlab Compiler Runtime in the container. I have worked
fs_time will not affect any processing, so you could replace it with a
stub. But why do you think it is fs_time?
On 3/19/2021 10:54 AM, Yakupov, Renat /DZNE wrote:
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Dear Freesurfer developers,
I am trying to run the longitudinal processing pipeline of
Right, it just wants the surface name (eg, white, pial)
On 3/19/2021 12:07 PM, Fischl, Bruce wrote:
HI Mudathir
Looks like mri_vol2surf doesn’t want the full path in the “surf”
parameter – just stuff after the “lh.”.
Cheers
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
*On
On 3/19/2021 12:03 PM, Alexopoulos, Dimitrios wrote:
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Just a further clarification between the using *conf2hires* or
*–hires * in FS7.1. Our data is acquired at 0.8mm isotropic.
In both cases are the surfaces
HI Mudathir
Looks like mri_vol2surf doesn’t want the full path in the “surf” parameter –
just stuff after the “lh.”.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ·
Sent: Friday, March 19, 2021 2:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer]
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Just a further clarification between the using conf2hires or -hires in
FS7.1. Our data is acquired at 0.8mm isotropic.
In both cases are the surfaces placed on the hi-res images, correct?
The subcortical structure volumes with con2hires are at
Have you looked at the segmentations on top of the anatomy? It might be
that they are so small that they sometimes don't get labeled.
On 3/19/2021 8:00 AM, 况况 wrote:
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TO: freesurfer@nmr.mgh.harvard.edu SUBJECT: mri_segstats error:
mri_extract_label mgz to
Can you send your command line and full terminal output?
On 3/18/2021 10:55 PM, Timothy Brackins wrote:
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Hello FreeSurfer Developers,
I am brand new to using freesurfer, just learning for the first time.
I have freesurfer installed and sourced on linux
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Dear Freesurfer developers,
I am trying to run the longitudinal processing pipeline of our data on our HPC
cluster (SGE based) and it crashes at the 3rd step - generating the
longitudinal runs. The exact command is 'recon-all -long tp1dir basedir
Hi Carolin
Yes, I guess send along images using all 3 orientations. There has to be some
white matter there somewhere….
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Caroline Chwiesko
Sent: Friday, March 19, 2021 12:28 AM
To: Freesurfer support list
Subject:
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You can do this with Connectome Workbench command (wb_command -surface-layer
and wb_command -volume-to-surface-mapping).
Matt.
From: on behalf of バキット・ムダシル
Reply-To: Freesurfer support list
Date: Friday, March 19, 2021 at 2:21 AM
To:
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TO: freesurfer@nmr.mgh.harvard.edu
SUBJECT: mri_segstats error: mri_extract_label mgz to nii
Hello FreeSurfer Developers,
I'm want to study the volume and function of amygdala subnucleis, so i need
to acquire the mask of amygdala subnucleis in
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Dear FreeSurfer users
I have been running the longitudinal pipeline with hippocampus
segmentation in FreeSurfer 7.1.1 on a computer cluster with a
batch-system that regulates number of cores to use. There is though a
problem when running
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?Hi Timothy,
Did you specify for -sd as well?
Best,
Raquel
Van: freesurfer-boun...@nmr.mgh.harvard.edu
namens Timothy Brackins
Verzonden: vrijdag 19 maart 2021 03:55
Aan: freesurfer@nmr.mgh.harvard.edu
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Dear freesurfer experts,
I want to create an equivolumetric surfaces (using the tool from:
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