AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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March 20, 2020 12:35PM
Hi, Neuro-

The parts preceding your SurfDist command seem correct.

Re. the SurfDist command:
+ "-i std.60.rh.pial.gii" does, indeed, specify the surface on which your node indices will be located.
+ why do you want "-Euclidian"? That would be the distance between the two points as a straight line *not* constrained to the surface. From previous questions, I would assume you want "-Graph" (or, just not putting either of these options, because "-Graph" is the default)?
+ the previous point probably relates to why nothing shows up with outputting a path, because you have not estimated distance along a path.

So, I ran (where "nodelist.1D" just contains "13020 14278", which I believe are your two node indices of interest):
SurfDist -i std.60.rh.pial.gii -input nodelist.1D -node_path_do PATH_DO
... which produced the following text output:
#Internodal distance along graph of surface std.60.rh.pial.gii
#A distance of -1 indicates an error of sorts.
#From   to     gDist.
 13020  14278  55.87
--> note how the distance along the surface is *longer* than the Euclidean distance, which makes sense-- dist_euclidean has to be less than or equal to the dist_alongsurf.

I could then view the PATH* as follows:
suma -onestate -i std.60.rh.pial.gii -sv MNI152_2009_SurfVol.nii &
DriveSuma -com viewer_cont -load_do PATH_DO.1D.do

Note: are you sure you want to use the pial surface for calculating distance? That is the "outer" GM boundary; it can be fine, but you have to choose whether you want the grey-white boundary, or the pial.

--pt
Attachments:
open | download - autorecord.A.200320_123122.522.jpg (68.1 KB)
Subject Author Posted

Distance between 2 coordinates via brain cortex

Neuro January 10, 2020 02:34AM

Re: Distance between 2 coordinates via brain cortex

ptaylor January 10, 2020 08:43AM

Re: Distance between 2 coordinates via brain cortex

Neuro January 23, 2020 06:09AM

Re: Distance between 2 coordinates via brain cortex

ptaylor January 23, 2020 09:11AM

Re: Distance between 2 coordinates via brain cortex

Neuro January 24, 2020 10:44AM

Re: Distance between 2 coordinates via brain cortex

ptaylor January 24, 2020 04:43PM

Re: Distance between 2 coordinates via brain cortex

Neuro January 25, 2020 04:33AM

Re: Distance between 2 coordinates via brain cortex

ptaylor January 25, 2020 01:32PM

Re: Distance between 2 coordinates via brain cortex

Neuro February 15, 2020 04:09AM

Re: Distance between 2 coordinates via brain cortex

ptaylor February 18, 2020 05:53AM

Re: Distance between 2 coordinates via brain cortex

Neuro March 07, 2020 05:10AM

Re: Distance between 2 coordinates via brain cortex

ptaylor March 08, 2020 04:30PM

Re: Distance between 2 coordinates via brain cortex

Neuro March 20, 2020 12:05PM

Re: Distance between 2 coordinates via brain cortex Attachments

ptaylor March 20, 2020 12:35PM

Re: Distance between 2 coordinates via brain cortex

Neuro March 20, 2020 09:09PM

Re: Distance between 2 coordinates via brain cortex

ptaylor March 21, 2020 08:26AM

Re: Distance between 2 coordinates via brain cortex

Neuro March 21, 2020 09:53PM

Re: Distance between 2 coordinates via brain cortex

ptaylor March 22, 2020 10:09AM

Re: Distance between 2 coordinates via brain cortex

Neuro March 30, 2020 11:45AM

Re: Distance between 2 coordinates via brain cortex

ptaylor March 30, 2020 11:57AM

Re: Distance between 2 coordinates via brain cortex

Neuro April 08, 2020 08:42PM