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Thank you, Douglas!
Kind regards,
Olga
> On Sep 13, 2022, at 3:41 PM, Douglas N. Greve wrote:
>
> Once you have the vertex number, you can get the MNI coordinate through some
> combination of operations shown on this page
> https://secure-web.cisco.
Once you have the vertex number, you can get the MNI coordinate through
some combination of operations shown on this page
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
Getting the minimum vertex is a little trickier. I would probably load
the thickness into matlab, eg,
thickness =
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Dear Experts,
I am looking for a way to extract information on the location (xyz coordinates
in MNI space) of a vertex with the lowest thickness value within an ROI (label)
for a group of subjects.
I have previously ran recon-all and qcache on the dat
have you looked at this page?
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 11/19/2021 9:15 AM, Gonzalo Rojas Costa wrote:
> External Email - Use Caution
>
> Hi:
>
>I have MNI 152 coordinates equivalent to 10-10 and 10-20 EEG
> electrodes (see Supplementary Tables 1 a
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Hi:
I have MNI 152 coordinates equivalent to 10-10 and 10-20 EEG
electrodes (see Supplementary Tables 1 and 2 in paper
https://secure-web.cisco.com/1h63DivIA2LKRlpONd2jZm_aVQOA0BCPi_yLJr4IOlwxEnAfG08DTJr4RESN6HNnmpW3-E_UvbeM3gHrvz45Ffp-ub6J_Np6lfVtQ-
It is probably easier to just run recon-all on the mni152, then use
mri_segcentroids on aparc.a2009s to extract the centroids
On 11/20/2020 2:50 AM, Hengameh Marzbani wrote:
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Hello Freesurfer developers,
For the purpose of reporting ROIs in my article, I
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Hello Freesurfer developers,
I have deadline time to report these coordinates.
I greatly appreciate your help and I'm looking forward to your kind response.
Best regards,
Hengameh
On Fri, Nov 20, 2020 at 11:20 AM Hengameh Marzbani
wrote:
> Hello
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Hello Freesurfer developers,
For the purpose of reporting ROIs in my article, I need a list of X Y
Z coordinates in MNI space for all the labels in the Destrieux atlas.
I came across a previous post with the following steps:
Step 1:
mri_annotation2l
orinna Bauer mailto:corinna...@gmail.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, February 28, 2020 at 9:26 AM
To: Mailing Freesurfer List
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] MNI coordinates from Thalamic nuclei
: *Friday, February 28, 2020 at 9:26 AM
> *To: *Mailing Freesurfer List
> *Subject: *[Freesurfer] MNI coordinates from Thalamic nuclei
>
>
>
> *External Email - Use Caution*
>
> Hi all,
>
> Is there a way to obtain the
Subject: [Freesurfer] MNI coordinates from Thalamic nuclei
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Hi all,
Is there a way to obtain the MNI coordinates for the thalamic nuclei?
Thanks
Corinna
The materials in this message are private and may contain Protected
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Hi all,
Is there a way to obtain the MNI coordinates for the thalamic nuclei?
Thanks
Corinna
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It is exactly what I want,
Thank you for your responsiveness and for your help,
Redwan
On Wed, Jul 26, 2017 at 12:14 PM, Douglas N Greve wrote:
> If you run it with --nofixmni, it will report MNI305 coords. Is that
> what you want?
>
>
> On 07/26/2017 03:11 PM, Redwan Maatoug wrote:
> > Hi all
If you run it with --nofixmni, it will report MNI305 coords. Is that
what you want?
On 07/26/2017 03:11 PM, Redwan Maatoug wrote:
> Hi all,
>
> My goal is to extract the coordinates from a .mgh ROI surface file.
>
> I have used this tool :
> mri_surfcluster with
>
> But the coordinates are in Ta
Hi all,
My goal is to extract the coordinates from a .mgh ROI surface file.
I have used this tool :
mri_surfcluster with
But the coordinates are in Tailarch and I would like the *MNI coordinates*.
Someone has an idea ?
Thank you,
Redwan
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You can create individual labels with mri_annotation2label from the
fsaverage annotation. The label is a text file with coordinate in it.
The coordinates will be MNI305 space. You can read these into matlab
with read_label.m. These will need to be converted to MNI152. See
http://surfer.nmr.mgh.
Hi All,
I am trying to visualise nodes of a brain network reconstructed using
FreeSurfer Desikan-Killiany Atlas parcellation scheme (aparc+aseg.mgz) on Brain
Net Viewer and Network Based Statistics software.
In order to do so, I need to upload a .txt file listing Freesurfer labels
coordinates
By default they are in talairach. But you can get mni305 by adding
--nofixmni to the surfcluster command line
On 08/02/2016 03:36 PM, Sabin Khadka wrote:
> Hi Doug, Thanks. Are these coordinates in talairach or MNI space? From
> previous post you mentioned these are in mni305 space but if I look
ps. you can always just load the xyz in the label into matlab and
compute the centroid
On 8/1/16 10:23 AM, Sabin Khadka wrote:
Anyone?
Cheers,
Sabin Khadka
On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka
mailto:mr.sabinkha...@gmail.com>> wrote:
Hi Doug, I tried to pick up from the threa
Try setting thmin to something small but non-zero (eg, 10e-6)
On 8/1/16 10:23 AM, Sabin Khadka wrote:
Anyone?
Cheers,
Sabin Khadka
On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka
mailto:mr.sabinkha...@gmail.com>> wrote:
Hi Doug, I tried to pick up from the thread below to get MNI
coo
Anyone?
Cheers,
Sabin Khadka
On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka
wrote:
> Hi Doug, I tried to pick up from the thread below to get MNI coordinates
> of each destrieux parcellation region.
>
>
>
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html
>
> I create
Hi Doug, I tried to pick up from the thread below to get MNI coordinates of
each destrieux parcellation region.
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html
I created label files from
mri_annotation2label --subject fsaverage --hemi lh(/rh) --annotation
aparc.a2009
here is one way
mri_cor2label --i aparc+aseg.mgz --id 10 --l left-thal.label
mri_label2label --srclabel ./left-thal.label --srcsubject subject
--trgsubject talairach --regmethod volume --trglabel left-thal.mni305.label
There will be an entry for each voxel in the label. The corrdinates in
left
Dear FS experts,
I would like to know the MNI coordinates of my ROIs obtained from recon-all
(aparc+aseg.mgz file). For example what for coordinates has number 10 (left
thalamus)? Are the coordinates of each region listed somewhere?
Many thanks for your help
Best wishes
André
eve
>> Sent: Thursday, September 25, 2014 11:57 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] MNI Coordinates
>>
>> multiply them by this matrix
>> $FREESURFER_HOME/average/mni152.register.dat
>>
>> On 09/25/2014 11:00 AM, Venkata
chana
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Thursday, September 25, 2014 11:57 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] MNI Coordinates
>
multiply them by this matrix
$FREESURFER_HOME/average/mni152.register.dat
On 09/25/2014 11:00 AM, Venkataraman, Archana wrote:
> Hi Freesurfer experts,
>
> I have a set of RAS coordinates in the Freesurfer fsaverage space. What is
> the easiest way to transform them to MNI152 space?
>
> Thanks.
>
Hi Freesurfer experts,
I have a set of RAS coordinates in the Freesurfer fsaverage space. What is the
easiest way to transform them to MNI152 space?
Thanks.
- Archana
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It was not in version 5.1, try 5.3 or let me know what platform you are
using and I can send it to you.
doug
ps. Please remember to post to the list and not to us personally. thanks!
On 9/17/13 2:09 AM, Simon Baker wrote:
Hi Doug,
There are several posts in which you mention the mri_surf
We don't have those number available, but you can generate them with
something like:
#1 Convert the annotation to a set of labels. This is for the Desikan
atlas, but you can spec the destrieux instead
mri_annotation2label --subject fsaverage --hemi lh --outdir ~/tmp/aparc
# For each label,
Hi
i am using corticals parcels (destrieux) as nodes in a connectivity study
using the NBS (Network Based Statistics) tool; i want to assign MNI coordinates
for these nodes. is there any MNI coordinates in freesurfer for each component
of this parcellation (not for every vertex in those comp
Hi Yolanda, you can run
mris_convert lh.white lh.white.asc
to produce a text file of the vertices and their coordinates. We also
have a matlab function to read in surfaces.
doug
On 06/20/2012 02:44 AM, Yolanda Vives wrote:
> Thank you Doug, I think that my question was not precise enough. I
> wo
Thank you Doug, I think that my question was not precise enough. I would
like to know which function I can use to obtain a vector with the number of
vertices and the corresponding MNI coordinates.
Regards,
Yolanda
2012/6/19 Douglas N Greve
> For fsaverage, the coordinates are the MNI305 coordin
For fsaverage, the coordinates are the MNI305 coordinates.
doug
On 06/19/2012 08:48 AM, Yolanda Vives wrote:
> Dear Freesurfer experts,
>
> How could I know the MNI coordinates of the 163.842 vertices of the
> left hemisphere of fsaverage?
>
> Best regards,
> Yolanda
>
>
>
> _
Dear Freesurfer experts,
How could I know the MNI coordinates of the 163.842 vertices of the left
hemisphere of fsaverage?
Best regards,
Yolanda
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Hi,
I created a surface label from fsaverage and would like to know its coordinates
in some commonly used space, such as e.g. talairach.
The vertex 6111 coordinates look like this:
611135.2, 1.9, -27.0 0
In tksurfer the coordinates of the vertex 6111 are:
Vertex RAS: (63.48 -12.29
Yes, but you'll need to create the matrix to do it. See
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.ppt
for more info.
doug
Yigal Agam wrote:
> Hi,
>
> Is it possible in matlab to get the volume index coordinates
> corresponding to
Hi,
Is it possible in matlab to get the volume index coordinates
corresponding to specific MNI coordiates?
Thanks,
Yigal
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