Dear Freesurfer Experts,

I've created a couple of ROIs from qdec comparisons of thickness and volume between two groups. We extracted the data from these ROIs for each subject using mris_anatomical_stats.

The stat files are located within each subjects folder:

sub/stats/rh.roi.stats

Now, we would like to combine the data from each stat file to a text file using aparcstats2table and asegstats2table (for volume measures). I already have batch scripts that call these functions for multiple subjects. The script basically concatenates all of the subject ids and inputs the concatenated string into the aparcstats2table (or asegstats2table) command.

EX:

asegstats2table -s s1 -s s2 -s s3 -s s4 --hemi lh --meas volume -tablefile test_stats.txt

I would like to modify my script so that I can extract the data from the roi.stats file. This is only a matter of entering the correct inputs for aparcstats2table and asegstats2table but I have tried with little success. The problems with each command are explained below.

For asegstats2table:

According to documentation (http://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table), I have tried running "asegstats2table $STRING --meas volume --skip --tablefile $OUTFILE " where string is "-i s1/stats/lh.roi.stats -i s2/stats/lh.roi.stats ......etc" but get the error message:

Building the table..

Traceback (most recent call last):

File "/Users/skip/Desktop/harlow_mount/apps/fmri_progs/freesurfer_v51/freesurfer/bin/asegstats2table", line 513, in <module>

rows, columns, table = sanitize_table(options, pretable)

File "/Users/skip/Desktop/harlow_mount/apps/fmri_progs/freesurfer_v51/freesurfer/bin/asegstats2table", line 412, in sanitize_table

_specs, _id_name_map, _measl = _t[0]

IndexError: list index out of range

For aparcstats2table:

when I run the command:

aparcstats2table $STRING --hemi lh --parc roi_name --skip --tablefile $OUTFILE

where string is "-s s1 -s s2 -s s3 ", I get a text file with 3 columns. The first column lists the subject ids, but what are the values for the 2nd and 3rd columns? Also, is it possible to input more than 2 .stats file for the command?

Looking forward to your responses,

Vy T.U. Dinh
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: Vy_dinh@rush.edu