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  

|
June 03, 2015 01:44PM
Hi-

The definitions are provided in the helpfile of 3dTrackID, under the description of the *.grid files. I probably shouldn't paste the helpfile, but I will, below.

  3) *.grid  ASCII-text file (output in ALL modes).
     Simple text file of output stats of WM-ROIs. It outputs the means and
     standard deviations of parameter quantities (such as FA, MD, L1, etc.)
     as well as counts of tracks and volumes of WM-ROIs. Each matrix is
     square, with dimension N_ROI by N_ROI. Like the locations in a standard
     correlation matrix, each element reflects associativity with target
     ROIs.  A value at element (1,3) is the same as that at (3,1) and tells
     about the property of a WM-ROI connecting target ROIs 1 and 3 (consider
     upper left corner as (1,1)); diagonal elements provide info of tracks
     through (at minimum) that single target ROI-- like OR logic connection.
     Format of *.grid file is:
     Line 1:  number of ROIs in network (padded with #-signs)
     Line 2:  number of output matrices of stats info (padded with #-signs)
     Line 3:  list of N_ROI labels for that network
     Lines following: first line, label of a property (padded with #), and 
                      then N_ROI lines of the N_ROI-by-N_ROI matrix of that
                      property;
                      /repeat/
     The first *five* matrices are currently (this may change over time):
         NT = number of tracks in that WM-ROI
         fNT = fractional number of tracks in that WM-ROI, defined as NT
               divided by total number of tracts found (may not be relevant)
         PV = physical volume of tracks, in mm^3
         fNV = fractional volume of tracks compared to masked (internally or
               '-mask'edly) total volume; would perhaps be useful if said
               mask represents the whole brain volume well.
         NV = number of voxels in that WM-ROI.
     Then, there can be a great variety in the remaining matrices, depending
     on whether one is in DTI or HARDI mode and how many scalar parameter
     files get input (max is 10). For each scalar file there are two
     matrices: first a label (e.g., 'FA') and then an N_ROI-by-N_ROI matrix
     of the means of that parameter in each WM-ROI; then a label (here,
     would be 'sFA') and then an N_ROI-by-N_ROI matrix of the standard
     deviations of that parameter in each WM-ROI.


NB: for exactness, I note that your definition (and similar for L2 and L3):
Quote
L1 - direction 1
isn't quite how I would phrase it; the eigen*vectors* (V1, V2, V3; or, sometimes written in papers as e1, e2, e3) provide the direction/orientation of each ellipsoid semiaxis; the eigen*values* (L1, L2, L3) are related to the amount of diffusion along each ellipsoid semiaxis.



--pt
Subject Author Posted

How to make multibrick ROI for 3dTrackID?

leetaey May 12, 2015 12:48AM

Re: How to make multibrick ROI for 3dTrackID?

ptaylor May 12, 2015 04:27AM

Re: How to make multibrick ROI for 3dTrackID?

leetaey May 12, 2015 08:35AM

Re: How to make multibrick ROI for 3dTrackID?

ptaylor May 12, 2015 09:26AM

Re: How to make multibrick ROI for 3dTrackID?

leetaey May 30, 2015 09:23PM

Re: How to make multibrick ROI for 3dTrackID?

ptaylor June 01, 2015 04:49PM

Re: How to make multibrick ROI for 3dTrackID?

leetaey June 01, 2015 06:34PM

Re: How to make multibrick ROI for 3dTrackID?

ptaylor June 02, 2015 06:42AM

Re: How to make multibrick ROI for 3dTrackID?

leetaey June 03, 2015 10:14AM

Re: How to make multibrick ROI for 3dTrackID?

ptaylor June 03, 2015 01:44PM

Re: How to make multibrick ROI for 3dTrackID?

leetaey June 10, 2015 11:20PM

Re: How to make multibrick ROI for 3dTrackID?

ptaylor June 10, 2015 11:55PM