How to use aparcstats2table and asegstats2table for rois generated from QDEC group analyses
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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_dinh@rush.edu mailto:Vy_dinh@rush.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
How did I miss this asegstats2table script? It looks great...and here I've been writing my own bash scripts to get the data out. - J
On Fri, May 18, 2012 at 1:59 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
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_dinh@rush.edu mailto:Vy_dinh@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 greve@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.
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Joshua Lee -
Vy Dinh