Here is a little script I wrote. It isn't very refined, and can be improved. It is also attached. It references a file you muct make in which you put all your subject names, one on each line of the text file like this:
sub001
sub002
sub003
...
Here is the script.
#run this script from the Freesurfer Subjects Directory...alterntively, you
can modify the script to work automatically
#from the the FreeSurfer Subjects Directory Variable. However, since you
might not be using the bash shell, maybe that variable wont be available.
Anyway..
filename=/home/local/AD3/jlee31/Desktop/NORA/segmentz #This points to a
file you will make in which every line contains a subject directory name.
#The script will read this file line by line to get the data from each
subject listed in the script
statsfile=rh.curv.stats #Tells the scipt which kind of stat files you want
to collect
#Name the file you want to put your results into
resultsFileName=results.txt
#Ok here we go
while read line; do
sub=`echo $line | cut -d\. -f1` #gets the subject name from the
file in the first line of this script
currentStatsFile=./"$sub"/stats/$statsfile #puts together the fullpath
of the stats file
#Next Grep finds a line in the file (stored in the variable
$myStatsFile) that mathces the criteria
#(for example here I find the line "Raw Total Surface Area:" and echos
that out to a result text file
echo $sub" "`grep "Raw Total Surface Area:" $currentStatsFile` #>>
$resultsFileName #creates a results txt file
done < "$filename"
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805
On Thu, May 17, 2012 at 2:37 PM, Vy Dinh <vy_d...@rush.edu> wrote:
> 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 <jki...@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_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
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>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
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>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>
getResults.sh
Description: Bourne shell script
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