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!
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 <thresh> in <overlayFile> and store in <label> for subject <subj> and hemisphere <hemi>:
$>mris_curvature_stats --highPassFilter <thresh> --filterLabel <label> <subj> <hemi> <overlayFile>
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
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!
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Lars M. Rimol -
Pratap Kunwar -
Rudolph Pienaar