[Freesurfer] getting vertex numbers
Hi,
I've done a glm model fit comparing cortical thickness between two
groups, and have certain areas ("blobs") on the cortical surface that are
above sig. threshold. I'd like to get a list of the vertex numbers for each
of these significant areas, which do not correspond to the parcellations in
FS. In other words, I'm not trying to combine the already excisting ROI's.
I've tried drawing labels (on fsaverage) and saving them, but without
success. I clicked on 'Make path' and tried to mark vertices around the
area, then I tried 'Custom fill' with various options, and 'Mark label',
'New label from marked' and 'save label'. But I only manage to save one or
at most 3-4 vertices.
I'm using FS v 4.0.5.
Any tip on how to do this would be appreciated!
Thank you!
--
yours,
LMR
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Re: [Freesurfer] getting vertex numbers
Hi,
Try like this,
Click inside your blobs.
Then click on the Custom Fill botton and then select "upto functional
value below threshold". This will select the cluster above the given p
value (1.3 in our case). Then click "fill".
Then click file->label->save selected label
this should work.
pratap
> Hi,
> I've done a glm model fit comparing cortical thickness between two
> groups, and have certain areas ("blobs") on the cortical surface that are
> above sig. threshold. I'd like to get a list of the vertex numbers for
> each
> of these significant areas, which do not correspond to the parcellations
> in
> FS. In other words, I'm not trying to combine the already excisting ROI's.
>
> I've tried drawing labels (on fsaverage) and saving them, but without
> success. I clicked on 'Make path' and tried to mark vertices around the
> area, then I tried 'Custom fill' with various options, and 'Mark label',
> 'New label from marked' and 'save label'. But I only manage to save one or
> at most 3-4 vertices.
>
> I'm using FS v 4.0.5.
>
>
> Any tip on how to do this would be appreciated!
>
> Thank you!
>
> --
> yours,
> LMR
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> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] getting vertex numbers
Lars M. Rimol wrote:
Hi,
I've done a glm model fit comparing cortical thickness between two
groups, and have certain areas ("blobs") on the cortical surface that
are above sig. threshold. I'd like to get a list of the vertex numbers
for each of these significant areas, which do not correspond to the
parcellations in FS. In other words, I'm not trying to combine the
already excisting ROI's.
I've tried drawing labels (on fsaverage) and saving them, but without
success. I clicked on 'Make path' and tried to mark vertices around the
area, then I tried 'Custom fill' with various options, and 'Mark label',
'New label from marked' and 'save label'. But I only manage to save one
or at most 3-4 vertices.
I'm using FS v 4.0.5.
Any tip on how to do this would be appreciated!
Thank you!
To get a label file containing only vertices above a certain threshold
in and store in for subject and
hemisphere :
$>mris_curvature_stats --highPassFilter --filterLabel
E.g. for subject 'MySubj' filter the 'lh.thickness' for all vertices
with "thickness" greater than 1.5, and store in 'lh.filter':
$>mris_curvature_stats --highPassFilter 1.5 --filterLabel lh.filter
MySubj lh thickness
will create a label file, 'lh.filter' containing a list of all vertices
whose "thickness" value exceeds 1.5
-=R
--
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
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Re: [Freesurfer] getting vertex numbers
Hi Lars,
you want to do "custom fill" then click the "over statistical threshold "
option. Can't remember the exact name...
cheers,
Bruce
On Wed, 18 Feb 2009, Lars M. Rimol wrote:
Hi,
I've done a glm model fit comparing cortical thickness between two
groups, and have certain areas ("blobs") on the cortical surface that are
above sig. threshold. I'd like to get a list of the vertex numbers for each
of these significant areas, which do not correspond to the parcellations in
FS. In other words, I'm not trying to combine the already excisting ROI's.
I've tried drawing labels (on fsaverage) and saving them, but without
success. I clicked on 'Make path' and tried to mark vertices around the
area, then I tried 'Custom fill' with various options, and 'Mark label',
'New label from marked' and 'save label'. But I only manage to save one or
at most 3-4 vertices.
I'm using FS v 4.0.5.
Any tip on how to do this would be appreciated!
Thank you!
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