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From: "Bruce Fischl";
Date: Wed, Apr 24, 2019 09:52 PM
To: "Freesurfer support list";
Subject: Re: [Freesurfer] recon-all error
hmmm, how long did you let it run? I've never seen this before. Can you
upload your subject to our ftp site?
cheers
Bruce
On Wed
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Dear freesurfer
We run the recon-all command of freesurfer, but when it runs to the
randomSeed 0 step below, it will not run anymore, that is, the running terminal
has been stuck in the following statement for more than 10 days.We want to ask
why t
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Dear Bruce,
Hello, we used mri_convert ?Cvs [] ?CI [] ?Co[] ?Crt interpolate to perform
the trilinear interpolation on the image, and also used the trilinear
interpolation in the torch to process the image. We found the result obtained
by the inter
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Dear Bruce??
I have fdr correction for sig.mgh obtained by mri_glmfit, but the corrected
graphs are all 0. Why is this, the instructions and the running results are as
follows:
mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh
lh2.gender
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Dear Bruce??
I have fdr correction for sig.mgh obtained by mri_glmfit, but the corrected
graphs are all 0. Why is this, the instructions and the running results are as
follows:
mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh
lh2.gender
diff.mgh
Best,
Tim
> On December 8, 2018 at 2:08 PM 1013364183 wrote:
>
>
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> Dear Bruce,
> I run the following command:
>
> mris_surface_stats -nsmooth 60 -surf_name $SUBJECTS_DIR/1001/surf/lh.white
> -out_na
ple the full command line you ran and the full output of it
(in text, not a screen shot!)
cheers
Bruce
On Sat, 8 Dec 2018, 1013364183 wrote:
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> The problem is in the fourth step of ThicknessRepea
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Dear Bruce,
I want to get the percent gray-white contrast((white-gray)/(white +
gray).100%) and gray intensity sampled at 30% cortical depth. What should I do?
yours yujunjie___
Freesurfer mailing list
Fre
ist";
: Re: [Freesurfer] Calculated thickness
Hi yujunjie
you can use mris_distance_transform -vol to compute a volumetric map of
distances to the surface if that is what you want.
cheers
Bruce
On Fri, 7 Dec 2018,
1013364183 wrote:
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>
e if that is what you want.
cheers
Bruce
On Fri, 7 Dec 2018,
1013364183 wrote:
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>
> Dear FS??
> I now have two different surfaces, the two surfaces have intersecting
> parts, I want to calculate
> their signed distance, what s
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Dear FS??
I now have two different surfaces, the two surfaces have intersecting parts,
I want to calculate their signed distance, what should I do?I want to calculate
the thick std and mean mgh files through mris_surface_stats, but there is no
outp
?
-- Original --
From: "Bruce Fischl";
Date: Mon, Dec 3, 2018 11:49 PM
To: "Freesurfer support list";
Subject: Re: [Freesurfer] Surface displacement
Hi yujunjie
you need to give us more information than this.
cheers
Bruce
On Mon, 3 Dec 201
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Dear FS,
We want to calculate the displacement of different surfaces, what should we do?
yours yujunjie___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/lis
: "Jonathan Polimeni";
: Re: [Freesurfer] ?? ?? ?? Triangular mesh samplingproblem
Hi yujunjie
I included him in the previous (and this) email
cheers
Bruce
On Sun, 2 Dec 2018,
1013364183 wrote:
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> Dear Bru
quot;Freesurfer support list";"Jonathan
Polimeni";
: Re: [Freesurfer] ?? ?? Triangular mesh sampling problem
hmm, maybe Jon (ccd) can help?
Bruce
On Sat, 1 Dec 2018, 1013364183 wrote:
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> Dear Bruce,
>
;t have any complete code that will do
exactly what you want though, so you will have to poke around in the source
yourself I'm afraid.
cheers
Bruce
On
Thu, 29 Nov 2018, 1013364183 wrote:
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> Dear Bruce,
> I want to do t
(maybe
someone else can?). The only alternative I can think of is to use the
various fsaverage meshes instead of the subject meshes. Then the
"projection" becomes trivial as the lower res meshes are just the first N
vertices in the higher res ones.
cheers
Bruce
On
ur own,
although it will be a bit of a project.
cheers
Bruce
On Tue, 6 Nov 2018, 1013364183
wrote:
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>
> Dear FS
> We now have high and low resolution images, we want to resample each
> triangular surface mesh
> ge
ischl";
: 2018??11??18??(??) 11:15
??: "Freesurfer support list";
: Re: [Freesurfer] ?? ?? Recon-all run error
Instructions on how you can upload tarred and gzipped files here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
On Sun, 18 No
quot;Freesurfer support list";
: Re: [Freesurfer] ?? ?? Recon-all run error
Instructions on how you can upload tarred and gzipped files here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
On Sun, 18 Nov
2018,
1013364183 wrote:
>
> Ex
licate and
fit ix.
On Tue, 6 Nov 2018, 1013364183 wrote:
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> Dear Bruce,
> I found the error location in the recon-all.log folder. Here is the place
> where it went wrong??I
> don't think it's the reason
or cerebellum still attached. Follow the tutorial for checking
for and fixing defects.
On 11/14/2018 02:59 AM, 1013364183 wrote:
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> Dear Bruce Fischl,
> I am very sorry that I have not reply to you last week.
> Our data has been running for
ischl";
: 2018??11??17??(??) 11:03
??: "Freesurfer support list";
: Re: [Freesurfer] multi-threaded question
Yes, use the -openmp option in recon-all
Cheers
Bruce
On Nov 16, 2018, at 9:52 PM, 1013364183 wrote:
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Dear FS,
I would like to ask if freesurfer can run multi-threaded. If so, can you give
us some guidance on this?
Thanks in advance
yours yujunjie___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
version of netcdf. I've attached a screenshot
of the code.
You could try setting all the soft limits for the shell to be unlimited, e.g.,
in bash,
$ ulimit -c unlimited
1013364183
November 5, 2018 at 21:22 via Postbox
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Dear FS
We now have high and low resolution images, we want to resample each triangular
surface mesh generated from low-resolution data onto the corresponding
triangular surface mesh generated from high-resolution data and vice versa as
follows: For
m. Can you run
the command that failed directly on the command line and see if it works?
Was anything else running on the machine at the time? We do report total
and free memory at the start of the recon in the recon-all.log file
cheers
Bruce
On Tue,
6 Nov 2018, 1013364183 wrote:
>
>
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Dear FS,
When we run ??recon-all?? with a 5GB high-resolution image, core dumped appears
when the mri_convert command is executed. The specific errors are as follows:
/opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 Aborted
(core
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