Hi Josh, Thanks for the sample script. With a few modifications to the variable definitions I got your script to work. However, my stats file looks like this:
# Table of FreeSurfer cortical parcellation anatomical statistics # # CreationTime 2012/05/10-17:03:40-GMT # generating_program mris_anatomical_stats # cvs_version $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ # mrisurf.c-cvs_version $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ # cmdline mris_anatomical_stats -l 051012_thickness_halluc_fwhm10_lh.fusiform.label -t lh.thickness -b -f 1014/stats/*051012_thickness_halluc_fwhm10_lh.fusiform.stats* 1014 lh # sysname Darwin # hostname skip-macpro-lab.rush.edu # machine i386 # user skip # # SUBJECTS_DIR /Users/skip/Desktop/harlow_mount/JenG/ResearchAssistant/data/freesurfer_v5.1 # anatomy_type surface # subjectname 1014 # hemi lh # AnnotationFile *051012_thickness_halluc_fwhm10_lh.fusiform.label* # AnnotationFileTimeStamp 2012/05/10 10:18:26 # Measure Cortex, NumVert, Number of Vertices, 119152, unitless # Measure Cortex, WhiteSurfArea, White Surface Total Area, 76575.4, mm^2 # NTableCols 10 # TableCol 1 ColHeader StructName # TableCol 1 FieldName Structure Name # TableCol 1 Units NA # TableCol 2 ColHeader NumVert # TableCol 2 FieldName Number of Vertices # TableCol 2 Units unitless # TableCol 3 ColHeader SurfArea # TableCol 3 FieldName Surface Area # TableCol 3 Units mm^2 # TableCol 4 ColHeader GrayVol # TableCol 4 FieldName Gray Matter Volume # TableCol 4 Units mm^3 # TableCol 5 ColHeader ThickAvg # TableCol 5 FieldName Average Thickness # TableCol 5 Units mm # TableCol 6 ColHeader ThickStd # TableCol 6 FieldName Thickness StdDev # TableCol 6 Units mm # TableCol 7 ColHeader MeanCurv # TableCol 7 FieldName Integrated Rectified Mean Curvature # TableCol 7 Units mm^-1 # TableCol 8 ColHeader GausCurv # TableCol 8 FieldName Integrated Rectified Gaussian Curvature # TableCol 8 Units mm^-2 # TableCol 9 ColHeader FoldInd # TableCol 9 FieldName Folding Index # TableCol 9 Units unitless # TableCol 10 ColHeader CurvInd # TableCol 10 FieldName Intrinsic Curvature Index # TableCol 10 Units unitless # ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd *051012_thickness_halluc_fwhm10_lh.fusiform.label* 85 76 435 3.697 0.350 0.325 0.129 6 0.5 I want to concatenate the last line for each subject, but since the string shows up 3 times in the stat file, I get more output info than I need. Is there a way to echo a line in the script only (using grep or some other command)? In other words, how can I only extract the last line from the stats file? Thanks, Vy On Thu, May 17, 2012 at 5:32 PM, Joshua Lee <jki...@ucdavis.edu> wrote: > 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 > >> > 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. > >> > > > > > > >
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