Thanks for the suggestion Josh! I have definitely thought about this, but since I'm a total novice bash programmer, I thought that it would be quicker to learn which option to add to asegstats2table and aparcstats2table. I would really appreciate it if you could help me come up with this code? What shell function could I use to open each .stats file? How do I use grep to call, say line 53 in the stats file?
Many thanks,
Vy
On Thu, May 17, 2012 at 4:19 PM, Joshua Lee jkilee@ucdavis.edu wrote:
Why not use a bash or csh script that loops through your subjects stat files, and use grep read the appropriate lines to a single text file with >>.
Josh
On Thu, May 17, 2012 at 1:04 PM, Vy Dinh vy_dinh@rush.edu wrote:
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
Vy T.U. Dinh Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu
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