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_d...@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_d...@rush.edu > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
