Try asegstats2table --stats=lh.roi.stats--meas volume --skip --tablefile $OUTFILE
doug On 05/17/2012 04:04 PM, Vy Dinh 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 <tel:%28312%29%20563-3853> > Fax: (312) 563-4660 <tel:%28312%29%20563-4660> > Email: vy_d...@rush.edu <mailto:vy_d...@rush.edu> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
