Re: [Freesurfer] pb reading .annot in matlab/python

hi doug,

this helps thanks. A next question is why can we have in the colortable a structureID that has no corresponding vertex with this label?

In my example it was 3834223 but I get the same thing with "fsaverage/label/lh.aparc.annot" that has a 3294840 structureID not present in the label array.

thanks Alex

On Tue, Aug 27, 2013 at 6:32 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

I think the 0s represent "unknown" areas. In this case, vertices that were not part of any cluster. Does that make sense? doug

On 08/27/2013 07:47 AM, Alexandre Gramfort wrote:

...

hi Doug,

I am sorry but I still don't get it.

If:

label vector lookup of annotation values for corresponding vertex index.

and label contains some 0 and 0 is not a valid id in colortable.table(:, 5) what should I do with my vertices whose label is 0?

thanks Alex

On Mon, Aug 26, 2013 at 11:52 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

...

ah, the newer version has a lot more info. See if this answers your question doug

help read_annotation NAME

     function [vertices, label, colortable] = ...
                                     read_annotation(filename [,

verbosity])

ARGUMENTS INPUT filename string name of annotation file to read

OPTIONAL verbosity int if true (>0), disp running output + if false (==0), be quiet and do not + display any running output

OUTPUT vertices vector vector with values running from 0 to + size(vertices)-1 label vector lookup of annotation values for + corresponding vertex index. colortable struct structure of annotation data + see below

DESCRIPTION

     This function essentially reads in a FreeSurfer annotation file
     <filename> and returns structures and vectors that together
     assign each index in the surface vector to one of several
     structure names.

COLORTABLE STRUCTURE

     Consists of the following fields:
     o numEntries:   number of entries
     o orig_tab:     filename of original colortable file
     o struct_names: cell array of structure names
     o table:        n x 5 matrix
                     Columns 1,2,3 are RGB values for struct color
                     Column 4 is a flag (usually 0)
                     Column 5 is the structure ID, calculated from
                     R + G*2^8 + B*2^16 + flag*2^24

LABEL VECTOR

     Each component of the <label> vector has a structureID value. To
     match the structureID value with a structure name, lookup the

row index of the structureID in the 5th column of the colortable.table matrix. Use this index as an offset into the struct_names field to match the structureID with a string name.

PRECONDITIONS

     o <filename> must be a valid FreeSurfer annotation file.

POSTCONDITIONS

     o <colortable> will be an empty struct if not embedded in a
       FreeSurfer annotation file.

On 08/26/2013 05:35 PM, Alexandre Gramfort wrote:

...

hi doug,

I thought so. Did I miss something obvious? My version is:

% read_annotation.m % Original Author: Bruce Fischl % CVS Revision Info: % $Author: nicks $ % $Date: 2011/03/02 00:04:12 $ % $Revision: 1.7 $

doc says:

colortable : Column 5 is the structure ID

Each component of the <label> vector has a structureID value.

Why do I get 0 in label if 0 is not in colortable.table(:, end)?

thanks Alex

On Mon, Aug 26, 2013 at 10:06 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

...

Hi Alex, have you looked at the read_annotation help? doug

On 08/26/2013 03:37 PM, Alexandre Gramfort wrote:

...

hi,

when trying to read the following .annot file:

https://dl.dropboxusercontent.com/u/2140486/annot_pb/left_mc-z.negative.sig....

using the following matlab code:

-- [vertices, label, colortable] = read_annotation('left_mc-z.negative.sig.ocn.annot'); unique(label) unique(colortable.table(:, end)) setdiff(colortable.table(:, end), unique(label)) --

there seem to be a discrepancy between the "label" and the last column of colortable "colortable.table(:, end)"

the script outputs:

-- Reading from version 2 colortable with 7 entries read (originally none) ans = 0 2244856 3987639 5840816 11298645 13698134 16665710 ans = 2244856 3834223 3987639 5840816 11298645 13698134 16665710 ans = 3834223 --

in other words 0 is in label but not in the colortable. Should I conclude that 0 is 3834223? If so what's the proper way of figuring this out?

thanks Alex _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/