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Dear Freesurfer experts,
Now I would like to find the peak vertex showed significant group effect in a given ROI (e.g. left insula), then draw a 5-mm-radius circle mask centred this peak point. May I know whether it is applicable and how should I do it with command line? Any suggestions would be much appreciated.
Best regards,
Lizhi
Hi Lizhi
the easiest way to approximate this is to generate a label that is just the peak vertex, then use the label editing tools in the current dev version of freeview to dilate it 4-5 times.
cheers Bruce
On Wed, 5 Jun 2019, Zhi Li wrote:
External Email - Use Caution
Dear Freesurfer experts,
Now I would like to find the peak vertex showed significant group effect in a given ROI (e.g. left insula), then draw a 5-mm-radius circle mask centred this peak point. May I know whether it is applicable and how should I do it with command line? Any suggestions would be much appreciated.
Best regards,
Lizhi
External Email - Use Caution
Hi Bruce,
Thank you very much for your kind reply. We have dozens of ROIs and hundreds of individuals, we need to draw the mask for each individual. May I know If I could do it in command lines? If it is applicable, which commands/functions should I refer to?
In addition, whether it is possible to use the index (16k+ for each surface) of this peak vertex in a annotation file to draw the mask? I am not clear how the index of each vertex ranked in a surface, could I found the index-vector of all the vertices in the circle mask centred the peak vertex? If circle is not applicable, how about square?
Best regards,
Lizhi
On Wed, 5 Jun 2019 at 11:51, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Lizhi
the easiest way to approximate this is to generate a label that is just the peak vertex, then use the label editing tools in the current dev version of freeview to dilate it 4-5 times.
cheers Bruce
On Wed, 5 Jun 2019, Zhi Li wrote:
External Email - Use CautionDear Freesurfer experts,
Now I would like to find the peak vertex showed significant group effect
in a given ROI (e.g. left
insula), then draw a 5-mm-radius circle mask centred this peak point.
May I know whether it is
applicable and how should I do it with command line? Any suggestions
would be much appreciated.
Best regards,
Lizhi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Lizhi
you could do it once on fsaverage then map the resulting label to all your subjects. They won't be circular in the individuals though (or really in fsaverage, but at least closer to circular). Or if you can find the peak vertex in each subject and create a label from it you can use mri_label2label which has a --dilate N option
cheers Bruce
On Wed, 5 Jun 2019, Zhi Li wrote:
External Email - Use Caution
Hi Bruce,
Thank you very much for your kind reply. We have dozens of ROIs and hundreds of individuals, we need to draw the mask for each individual. May I know If I could do it in command lines? If it is applicable, which commands/functions should I refer to?
In addition, whether it is possible to use the index (16k+ for each surface) of this peak vertex in a annotation file to draw the mask? I am not clear how the index of each vertex ranked in a surface, could I found the index-vector of all the vertices in the circle mask centred the peak vertex? If circle is not applicable, how about square?
Best regards,
Lizhi
On Wed, 5 Jun 2019 at 11:51, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Lizhi
the easiest way to approximate this is to generate a label that is just the peak vertex, then use the label editing tools in the current dev version of freeview to dilate it 4-5 times. cheers Bruce On Wed, 5 Jun 2019, Zhi Li wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > Now I would like to find the peak vertex showed significant group effect in a given ROI (e.g. left > insula), then draw a 5-mm-radius circle mask centred this peak point. May I know whether it is > applicable and how should I do it with command line? Any suggestions would be much appreciated. > > Best regards, > > Lizhi > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Bruce,
Thanks. I found a command from a previous post which seems capable of generating a surface data file in which all the vertices = 0 except the peak vertex:
mri_volsynth --temp $SUBJECTS_DIR/yoursubject/surf/lh.curv --pdf delta --delta-crsf vertexno 0 0 0 --o delta.mgh
I could run this command but I am not clear how to change the vertexno, what the three zeros denotes? If the index of my vertex is 1500 in fsaverage, how should I change above command accordingly? In addition, what are the meanings of flag "--pdf" and "delta"? I did not found the description in the "mri_volsynthn".
Best regards,
Lizhi
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Zhi Li