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Hello FreeSurfer Developers,
I run the recon-all -all command for aboout 10 hours.1. I want to accelerate,
is there any way, such as how to achieve multi-core parallelism? Or is there
another way to speed things up?
2. What are the quick ways to
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Thanks Doug - yes, I'd like the vertex coordinates in the same format as
the local subject surface files are in.
On 07/05/2020 19:02, Douglas N. Greve wrote:
It comes down to how you want to define "roughly in the same place".
Does this mean an
rom
:%22Douglas+N.+Greve%22> Douglas N. Greve
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date
:20200507> Thu, 07 May 2020 14:56:08 -0700
sorry, please include the previous email chain so that I know what you are
referring to
On 5/7/2020 5:33 PM, Xiaojian
sorry, please include the previous email chain so that I know what you
are referring to
On 5/7/2020 5:33 PM, Xiaojiang Yang wrote:
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Douglas,
Just as I mentioned in the initial email, subjects in the healthy
group have different ages. Because average
Isn't that what you got from the mri_surf2surf command?
On 5/7/2020 3:08 PM, Ian Hardingham wrote:
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Thanks Doug - yes, I'd like the vertex coordinates in the same format
as the local subject surface files are in.
On 07/05/2020 19:02, Douglas N. Greve
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Douglas,
Just as I mentioned in the initial email, subjects in the healthy group have
different ages. Because average cortical thickness is believed to be
declined as the age gets older, I want to "normalize" the group by
multiplying each subject's
I don't know what weight is. Can you elaborate?
On 5/7/2020 4:54 PM, Xiaojiang Yang wrote:
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Hi Douglas,
Thank you very much! Could you please help me with more detailed
information?
1)Should I use “Variables age” or “Variables age weight” in the fsgd
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Hi Douglas,
Thank you very much! Could you please help me with more detailed
information?
1) Should I use "Variables age" or "Variables age weight" in the fsgd
file? If I can use either of them, which one is better?
2) For the contrast
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Hello Gonzalo,
If you don’t mind using Ubuntu 18 as the OS in the virtual machine, then we
already have a virtual machine you can run with virtualbox that is close to
what you want. It has the previous version 7 beta 1 release of
freesurfer (and
Sorry, we are no longer supporting CUDA. Too much of a moving target.
That flag should have been deleted (and will be in future updates)
On 5/7/2020 3:58 PM, Mina Rizkallah wrote:
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Hello again,
I successfully installed FreeSurfer 7 on Centos 8 and it
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Hello again,
I successfully installed FreeSurfer 7 on Centos 8 and it works smoothly.
my concern is regarding the CUDA compatibility, in recon-all help I found the
(-use-gpu) flag is present but when I tried to use it, I got error for
unrecognized
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From: Timothy Coalson
Reply-To: Timothy Coalson
Date: Thursday, May 7, 2020 at 2:30 PM
To: "Glasser, Matthew"
Cc: Freesurfer support list
Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
The way to map data between freesurfer and
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I'd like to get a set of points to compare across several brains, so
that the nth point in brain A is in roughly the same place as the nth
point in brain B - so I'd like to have an agreed upon set of vertices
(the source brain's vertices) translated
I think it will work properly if you use the raw data as input and
create an FSGD file with two classes: (1) the individual subject and (2)
healthy subjects. Also include age as a covariate. Use DOSS instead of
DODS. Then set your contrast to be 1 -1 0 and run mri_glmfit. I think
that should
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Dear FS experts,
I have a group of healthy subjects. Given a new individual subject, I want
to compare its cortical thickness to the healthy group so that I can find
where the thickness is abnormal (thickening or thinning).
I use fsaverage as the
It comes down to how you want to define "roughly in the same place".
Does this mean an affine (12dof) transform? And what information do you
want? An XYZ coordinate?
On 5/7/2020 11:06 AM, Ian Hardingham wrote:
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I'd like to get a set of points to compare
It looks like mris_convert will do, but I've never tried it.
On 5/7/2020 1:23 PM, Glasser, Matthew wrote:
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Hi Doug,
Is there a way to convert from GIFTI label to annot?
Matt.
*From: * on behalf of "Douglas
N. Greve"
*Reply-To: *Freesurfer support
> External Email - Use Caution
>>
>> HCPMMP1 parcellation is multi modal parcellation
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990127/
>>
>> We need the file something like we have for 'aparc' parcellation.
&g
gt;
> We need the file something like we have for 'aparc' parcellation.
> The file format should be in .mgz (aparc.HCPMMP1+aseg.mgz)
> How can i do it? (i have lh.HCPMMP1.annot and rh.HCPMMP1.annot)
>
> --
> Thank You
> Pooja Prabhu
> ---
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Hi Doug,
Is there a way to convert from GIFTI label to annot?
Matt.
From: on behalf of "Douglas N. Greve"
Reply-To: Freesurfer support list
Date: Thursday, May 7, 2020 at 12:21 PM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer]
If you have the annot files in your individual subject's space, then you
can create a volume in the same way that aparc+aseg.mgz is created. In
v6 and before, run mri_aparc2aseg. In v7, run mri_surf2volseg. Look in
recon-all.log to see how it was run to craeate aparc+aseg.mgz and change
the
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>HCPMMP1 parcellation is multi modal parcellation
>We need the file something like we have for 'aparc' parcellation.
>The file format should be in .mgz (aparc.HCPMMP1+aseg.mgz)
>How can i do it? (i have lh.HCPMMP1.annot and rh.HCPMMP1.annot)
Date:
Hi Julien,
Just to test something out, can you try running this again after replacing the
flirt.fsl binary in your new 7.0 install with the flirt.fsl binary from 6.0?
i.e.
cp /path/to/freesurfer/6.0.0/bin/flirst.fsl
/path/to/freesurfer/7.0.0/bin/flirst.fsl
Let me know how that works.
Best
Does
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/label/lh.cortex.label
exist?
On 5/7/2020 11:33 AM, Mason Wells wrote:
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Terminal output is below:
export
SUBJECTS_DIR=/home/c1749990/Documents/Analysis/Data/freesurfer/subjects
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Hi:
No... I don't have any specific issue... I have a previous freesurfer
version installed that I want to continue using. So I want to install
version freesurfer 7.0 on a virtual machine...
Sincerely,
Gonzalo Rojas Costa
> Message: 4
> Date:
sorry, can you include the previous emails?
On 5/7/2020 11:25 AM, pooja prabhu wrote:
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HCPMMP1 parcellation is multi modal parcellation
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990127/
We need the file something like we have for 'aparc' parcellation.
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HCPMMP1 parcellation is multi modal parcellation
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990127/
We need the file something like we have for 'aparc' parcellation.
The file format should be in .mgz (aparc.HCPMMP1+aseg.mgz)
How can i do it? (i
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That is our multi-modal parcellation. Tim has some instructions to get data
from the fs_LR mesh to fsaverage in GIFTI format. Doug perhaps you can say how
to convert from GIFTI to annot?
Matt.
From: on behalf of "Douglas N. Greve"
Reply-To:
conf2hires is in version 7. Use the -conf2hires flag. If you have an
error message, it would be most helpful if you share it with us
On 5/7/2020 6:29 AM, Dr. Ilona Lipp wrote:
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>
> Hi,
> in the version 7 release notes it says this: "conf2hires. This is an
what's hcpmmp1?
On 5/7/2020 4:46 AM, pooja prabhu wrote:
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Hai list,
Can I get some insight on how to convert HCPMMP1 to aseg(provided we
have annotation files) for fsaverage brain?
For example: for aparc parcellation we use aparc2aseg and get
I don't understand. What is the difference between the target brain and
the target subject's vertices?
On 5/7/2020 2:17 AM, Ian Hardingham wrote:
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Ok, thanks Doug, but I'm looking to get the positions of the source
vertexes on the target brain, not the
No all, just one. And try running it with just the -parcstats3 flag (ie,
don't use -all or -autreconX). You should have an answer in seconds
On 5/7/2020 7:50 AM, Mason Wells wrote:
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Hi Doug,
Sorry I am a bit confused. I ran recon-all as a bash for 30
it looks to me like recon-all finished without a problem. Have you looked
at the outputs? Is there another reason you think there is an issue? There
are lots of internal "error" metrics we use to optimize things that are not
errors in the programatic sense - they are functionals we are
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Hi,
I just installed freesurfer v7 and I'm getting an error in a script that
calls bbregister with the --fslmat and --init-fsl options. This error
does not occur in freesurfer v6 even when using exactly the same data,
but it does also occur with a
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Hi Doug,
Sorry I am a bit confused. I ran recon-all as a bash for 30 participants. None
of which had the right hemisphere completed and recon-all log says exited with
errors (as the log in the original email shows). Are you suggesting I go back
and
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There should be no difference to installation on a physical machine. Are you
running into any specific issues?
Tim
> On May 7, 2020 at 3:51 AM Gonzalo Rojas Costa
> wrote:
>
>
> External Email - Use Caution
>
> Hi:
>
> How
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Hi,
in the version 7 release notes it says this: "conf2hires. This is an
alternative method to do hi-res recon byrunning part of the stream at 1mm, then
placing the 1mm surfaces on the hi-res volume. This was originally programmed
for the HCP. The
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Ok, thanks Doug, but I'm looking to get the positions of the source
vertexes on the target brain, not the target subject's vertices...
On 06/05/2020 23:07, Douglas N. Greve wrote:
That looks like it could be right. It has 102,020 vertices, which
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Hai list,
Can I get some insight on how to convert HCPMMP1 to aseg(provided we have
annotation files) for fsaverage brain?
For example: for aparc parcellation we use aparc2aseg and get
aparc+aseg.mgz.
Similarly I need for HCPMMP1.
Can someone help me
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