list ;
Zollei, Lilla,Ph.D.
*Subject:* Re: [Freesurfer] mris_register external atlas
*External Email - Use Caution *
Hi Bruce,
Thanks. The command seems to stall when I try to run it following
mri_surf2surf.
It ends like this: "calling annotation2labelV2() ..." And then doesn
Sorry, I defer to Doug...
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Stefanie Bradley
Sent: Wednesday, April 2, 2025 3:52 PM
To: Freesurfer support list ; Zollei,
Lilla,Ph.D.
Subject: Re: [Freesurfer] mris_register external atlas
External Email - Use Caution
Hi Bruce
@nmr.mgh.harvard.edu
Subject: [Freesurfer] mris_register external atlas
External Email - Use Caution
Hi there,
I am trying to register my Freesurfer subject's cortical surface into a common
space to use the parcellations from a pediatric atlas (UNC 4D cortical surface
atlas).
Sent: Monday, March 31, 2025 4:41 PM
To: Freesurfer support list
Cc: Zollei, Lilla,Ph.D.
Subject: Re: [Freesurfer] mris_register external atlas
You don't often get email from bfis...@mgh.harvard.edu. Learn why this is
important<https://secure-web.cisco.com/1n0q7-5_MhqbUSwkqp2HOBEIE
To: Freesurfer support list
Cc: Zollei, Lilla,Ph.D.
Subject: Re: [Freesurfer] mris_register external atlas
You don't often get email from bfis...@mgh.harvard.edu. Learn why this is
important<https://secure-web.cisco.com/1gfZq
is a bug?
Stef
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Fischl, Bruce R.,PHD
Sent: Wednesday, April 2, 2025 3:42 PM
To: Freesurfer support list ; Zollei,
Lilla,Ph.D.
Subject: Re: [Freesurfer] mris_register external atlas
You don't often get email from bfis...@mgh.harvard
gt;;
Zollei, Lilla,Ph.D. mailto:lzol...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] mris_register external atlas
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important<https://secure-web.cisco.com/1PHsQ
Fischl, Bruce R.,PHD
Sent: Wednesday, April 2, 2025 3:22 PM
To: Freesurfer support list ; Zollei,
Lilla,Ph.D.
Subject: Re: [Freesurfer] mris_register external atlas
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Subject: Re: [Freesurfer] mris_register external atlas
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Thank you, that worked!
To recap, I've been trying to align the annotation files from the UNC cortical
surface atlas to my subjects. I'm using Freesurfer version 8.0.0 with Linux.
Following mri
ices. Is there a way to fix
this so that I can proceed?
Thanks,
Stefanie
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Fischl, Bruce R.,PHD
Sent: Monday, March 31, 2025 4:41 PM
To: Freesurfer support list
Cc: Zollei, Lilla,Ph.D.
Subject: Re: [Frees
External Email - Use Caution
Hi there,
I am trying to register my Freesurfer subject's cortical surface into a common
space to use the parcellations from a pediatric atlas (UNC 4D cortical surface
atlas).
With Freesurfer version 8.0.0 in a Linus OS, I am using mris_register as:
d.edu
*Subject:* [Freesurfer] mris_register options
*External Email - Use Caution *
Dear Doug
Dear Bruce
Martin Reuter suggested me to write you since you are familiar with
true inner workings of free surfer. In my project I try to create a
family specific template that is based on three or
Sent: Monday, May 8, 2023 8:01 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mris_register options
External Email - Use Caution
Dear Doug
Dear Bruce
Martin Reuter suggested me to write you since you are familiar with true inner
workings of free surfer. In my project I t
External Email - Use Caution
Dear Doug
Dear Bruce
Martin Reuter suggested me to write you since you are familiar with true inner
workings of free surfer. In my project I try to create a family specific
template that is based on three or more family members. We try to avoid the
Hi Danny
yes, you can specify up to 100 labels. Make sure that the label name is
exactly as it appears in the parcellation though
cheers
Bruce
On Wed, 27 May 2020, Danny
Kim wrote:
External Email - Use Caution
Hi FreeSurfer experts,
I'm currently working on a brain with
External Email - Use Caution
Hi FreeSurfer experts,
I'm currently working on a brain with a bit of atypical morphology and was
wanting to parcellate through the DKT labels, but by using manually drawn
labels as guides. The intent here is to fix specific labels to be where they
External Email - Use Caution
Yeah that works, thanks a lot.
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Friday, 22 May 2020 1:08 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_register intermediate results display
I
Hi Chris
if you specify -w on the command line it will write out a surface
every n iterations of the minimization (-n 1 will write out every step).
You can then write a script to turn those into tiffs with freeview
cheers
Bruce
On Thu,
21 May 2020, Chris Adamson wrote:
External
I would just map the ?h.curv from one subject to another and then
display them on a single surface and flip back and forth. Would that
work for you?
On 5/21/2020 9:30 AM, Chris Adamson wrote:
External Email - Use Caution
Freesurfer devs,
Apologies if this has already been asked. I’m
External Email - Use Caution
Freesurfer devs,
Apologies if this has already been asked. I'm looking for a way that I can look
at the progress of mris_register to investigate the accuracy of registration.
Given that the registration is done on the 2D parameterisations of the
cur
ad to increase the angular search range in the affine part to get it to work.
Cheers,
Chris.
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of
Bruce Fischl
Sent: Monday, 17 September 2018 11:49 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_register problem
Hi
list
Subject: Re: [Freesurfer] mris_register problem
Hi Chris
you need to give us more information. What commands did you run? What was
their output? Also, if you can send images of what you think is incorrect
that might also be helpful
cheers
Bruce
On Mon, 17 Sep 2018, Chris Adamson wrote
Hi Chris
you need to give us more information. What commands did you run? What was
their output? Also, if you can send images of what you think is incorrect
that might also be helpful
cheers
Bruce
On Mon, 17 Sep 2018, Chris Adamson wrote:
External Email - Use Caution
Frees
External Email - Use Caution
Freesurfer experts,
I'm having an issue with projecting labels from an atlas to a subject. I have a
static annot file on the atlas that I want to paint onto my subject. The
pipeline I have performed is to mris_register my subject to the atlas and the
Hi Francois, this is an mris_register bug from last month that should be fixed
in the most recent dev distribution.
best,
Andrew
From: on behalf of "Lalonde, Francois
(NIH/NIMH) [E]"
Reply-To: FS Help
Date: Tuesday, August 7, 2018 at 2:33 PM
To: FS Help
Subject: [Freesurfer] mri
Hi Jürgen
surfreg is a wrapper around mris_register.
cheers
Bruce
On Fri, 18 Aug 2017, Juergen
Haenggi wrote:
Dear FS experts
we constructed a customized template (using make_average_subject) to
register the individual surfaces on that template instead of the fsaverage
template.
we recognize
Dear FS experts
we constructed a customized template (using make_average_subject) to register
the individual surfaces on that template instead of the fsaverage template.
we recognized that there are, at least, two ways to do this either using
mris_register or using surfreg.
Is there any differe
yes, I believe that is true
On Thu, 20 Oct 2016, Nicholas Heugel wrote:
So just to be clear, If the individual cortical parcellations are accurate then
what we observe isn't
due to some quirk from the cross subject registration?
Nicholas HeugelBiomedical Engineering Ph.D Candidate
Marquette
So just to be clear, If the individual cortical parcellations are accurate
then what we observe isn't due to some quirk from the cross subject
registration?
Nicholas Heugel
Biomedical Engineering Ph.D Candidate
Marquette University
On Thu, Oct 20, 2016 at 4:32 PM, Bruce Fischl
wrote:
> Hi Nicho
Hi Nicholas
I wouldn't think so. Look at the cortical parcellations and see if they
are accurate. If they are it means that the cross-subject registration
must be pretty good
Bruce
On Thu, 20 Oct 2016, Nicholas Heugel wrote:
I am encountering an odd effect when using the Freesurfer maps in B
I am encountering an odd effect when using the Freesurfer maps in
Brainstorm. I have Individual activity for multiple subjects where the
activity generally seems to look generally well spread across teh gyrus and
sulcus in task relevant areas. However, when I map the individual subjects
onto the
Hi,
I've had time to come back to this problem. It was not solved after
recreating the sphere. And plus, it happens in 30% of my subjects
(Approximately).
I have opened the sphere and I can see no problem there (nor there is any
kind of error message after opening it.
Could you tell me what file
try opening it in tksurfer and see if it complains
On Sun, 2 Aug 2015, Fidel
Alfaro Almagro wrote:
Hi,
Thanks for the quick answer.
There was no error message in the previous steps.
I started it with : mris_sphere -seed 1234 ../surf/lh.inflated
../surf/lh.sphere
Although if the seed is the
Hi,
Thanks for the quick answer.
There was no error message in the previous steps.
I started it with : mris_sphere -seed 1234 ../surf/lh.inflated
../surf/lh.sphere
Although if the seed is the same, I am guessing that any non-deterministic
process would have the same output.
Is there a a way to
hmm, something seems to be wrong maybe the the ?h.sphere. Can you try
recreating it
cheers
Bruce
On Sun, 2 Aug 2015, Fidel Alfaro Almagro wrote:
Hi all,
I received an error in one of the steps of recon-all. The error is "No such
file or directory" at the end of one of the registration processe
Hi all,
I received an error in one of the steps of recon-all. The error is "No such
file or directory" at the end of one of the registration processes.
The step was mris_register -curv. The command was:
mris_register -curv ../surf/lh.sphere
/average/lh.average.curvature.filled.buckner40.tif
../s
Hi, freesurfer developers.
I've downloaded the source code from the read-only CVS repository and built
them to analyze my own subject data.
The problem is that running recon-all with the example subject 'bert' fails
sometimes.
I'd investigated this further and see the follownigs I'd found and le
Hi Greg,
try using recon-all -make all
then rerun the V1 stuff.
cheers
Bruce
On Tue, 9 Mar 2010, Gregory Dierksen wrote:
>
> Hello,
>
> So I'm attempting to use the V1_predict script to generate a primary
> visual cortex label and had been receiving an error message. I was able
> to track down
Hello,
So I'm attempting to use the V1_predict script to generate a primary
visual cortex label and had been receiving an error message. I was able
to track down the error to the mris_register command:
mris_register -inflated -a 4096 -dist 10.0 -parea 1.0 \
/surf/lh.sphere \
/label/lh
Hi XJ,
if you specify -n 0 I think it will not run the nonlinear.
cheers,
Bruce
On Fri, 7 Dec 2007, XJ Kang
wrote:
Hi,
I am trying to register the spheres to the template. The current version
of mris_register may have some nonlinear local deformation of the gyral
and sulcal structure. Anyw
Hi,
I am trying to register the spheres to the template. The current version
of mris_register may have some nonlinear local deformation of the gyral
and sulcal structure. Anyway I can specify the "rigid alignment" only? I
didn't find the option for linear alignment only after checking the
options
Hi Colleen,
-parea sets the coefficient on the area term, and the -dist sets the
coeffcient on the distance term. I think the defaults are:
aligning to individual template: parea=.1, dist=.5
aligning to group template:parea=0.2, dist=.1
in general the dist (metric preservation) is a mu
Good afternoon,
Could anyone out there tell me what exactly the -parea and -dist
options to mris_register do?
I'm working on a project comparing across a large number of brains
and would like to find the optimal registration parameters before
running all the morphs. But I wasn't able to get any
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