Hi Rick & Ziad,
sorry for the delay we became sidetracked.

To recap, in freesurfer we created label files for the structural parcelated brain for the entire thickness of gray matter (not just the interface btwn gray and white) As was submitted previously:

The label files we are using in the tkmedit viewing tool contain zeros in the first column (the node index column). For example, the first line reads as follows (viewed through MORE).

0 53.000 -31.000 49.000 0.000000

You are correct, the middle 3 columns are RAI coordinates, and the 1st and 5th olumns are zeros --so there is no node information. --you suggested creating an index column for the 1st column, using the last column (via the -sdata_1D option) but we aren't sure what the 5th column is supposed to be-- [Your former reply is at the bottom of this email.]

We would like to bring these files into AFNI and/or SUMA.
How can we do this?

Thank you for your help
Jennine





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Hi Jennine,

1. So what you have is an xyz-coordinate file, which you
want to use as the surface in 3dSurf2Vol, is that right?

Assuming the answer is yes...

2. Are the coordinates in RAI orientation? i.e. does the
coordinate (53.000 -31.000 49.000) mean 53 mm left, 31 mm
anterior and 49 mm superior?

3. If "no" to #2, does the orientation match that of the
AFNI dataset that you plan to use for the '-grid_parent'
option?

4. You have 5 columns in that file. Is the last column
intended to be used for data (via the '-sdata_1D' option)?
If so, then it may be necessary to replace the initial zero
column with an index column (easy to do, via 'awk').

In any case, if the answer to #1 is "yes", then I should
mention that I broke that functionality going to version
3.0. On the plus side, it's fixed... :)

- rick