Hi Alessandro,

To view data from R in tksurfer, we did this:

1.) wrote a table from R containing the data values we wanted to visualize, all in one column, with the same number of values as there were nodes in the anatomical brain (either individual or fsaverage).

1.5.) i can't remember, but it may have been necessary to round off the values in this column to 5 decimals in R

2.) pasted that column with the first 4 columns from an ascii file that had been previously converted with mris_convert from .mgh data for the same subject. these four columns contained the node indices, and 3 coordinates (is this clear? you take some .mgh format data for the subject, convert to .asc and you get 5 columns. here you only want the first four, and then you paste the last which contains your new data from R)

3.) converted the new text document (with all 5 columns, and extension .asc) to .mgh using the new mris_convert that doug pointed us to here:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_convert

when we did it this way, the .mgh files loaded in tksurfer. hope this helps!

emily

On 4/3/07, Alessandro Gagliardi alessandro@gagliardi.name wrote:

Hello Emily and other FreeSurfer useRs,

I'm having trouble getting data out of R and back into FreeSurfer and I was wondering how you did it. The tksurfer doesn't seem to like the .img files that the AnalyzeFMRI package produces (perhaps because it doesn't have a .mat file to go with it). I've tried to convert ascii files into Analyze and MGH files using mris_convert, but tksurfer doesn't like those either.

Any help would be greatly appreciated. Thanks!

Alessandro Gagliardi Integrative Neuroscience Program Rutgers University Mind Brain Analysis alessandro@gagliardi.name