Thanks Doug. So I change the command line syntax to the following: csh::alanf@cerebro [/media/Alan_WORK/WORK/De_LISI_Final/LGI_HSF] : aparcstats2table --hemi lh --subjects /HM0403 /HM0503 /HM0603 /HM0703 /HM0903 /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 /HM2103 /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 /HM3103 /HM3202 /HM3203 /HM3303 /HM3403 /HM3503 /HM3603 /HM3703 /HM3903 /HM4003 /HM4203 /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 /HM4803 /HM4903 /HM5103 /HM5203 /HM5303 /HM5403 /HM5503 /HM5603 /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 /HM6303 /HM6403 /HM6503 /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 /HM7203 /HM7303 /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 /HM8203 /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 --parc BA --meas thickness --tablefile BA_LGI.txt
SUBJECTS_DIR : /media/Alan_WORK/WORK/De_LISI_Final/LGI_HSF/ Parsing the .stats files ERROR: The stats file /HM0403/stats/lh.BA.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files csh::alanf@cerebro [/media/Alan_WORK/WORK/De_LISI_Final/LGI_HSF] : When I use the -- skip flag it skips all the lh.BA.stats files. I am using FreeSurfer 5.0. thanks so much, Alan On Tue, Sep 3, 2013 at 11:59 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > > > Your comamnd line is incorrect. Use --subjects instead of -s. Or just use > only the --subjectsfile. > doug > > > > On 09/03/2013 11:55 AM, Alan Francis wrote: > >> Hi Doug: >> >> Here is the message it gives. It's not so much an error message as an >> advisory on usage. >> >> thanks so much, >> >> Alan >> >> aparcstats2table --hemi lh -s HM0403 /HM0503 /HM0603 /HM0703 /HM0903 >> /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 /HM2103 >> /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 /HM3103 /HM3202 >> /HM3203 /HM3303 /HM3403 /HM3503 /HM3603 /HM3703 /HM3903 /HM4003 /HM4203 >> /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 /HM4803 /HM4903 /HM5103 /HM5203 >> /HM5303 /HM5403 /HM5503 /HM5603 /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 >> /HM6303 /HM6403 /HM6503 /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 >> /HM7203 /HM7303 /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 >> /HM8203 /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 >> --parc BA --meas FoldInd --tablefile BA44 BA45 --subjectsfile=BA_LGI.txt >> >> Usage: >> Converts a cortical stats file created by recon-all and or >> mris_anatomical_stats (eg, ?h.aparc.stats) into a table in which >> each line is a subject and each column is a parcellation. By >> default, the values are the area of the parcellation in mm2. The >> first row is a list of the parcellation names. The first column is >> the subject name. >> >> The subjects list can be specified on either of two ways: >> 1. Specify each subject after a -s flag >> >> -s subject1 -s subject2 ... --hemi lh >> >> 2. Specify all subjects after --subjects flag. --subjects does not have >> to be the last argument. Eg: >> >> --subjects subject1 subject2 ... --hemi lh >> >> By default, it looks for the ?h.aparc.stats file based on the >> Killiany/Desikan parcellation atlas. This can be changed with >> '--parc parcellation' where parcellation is the parcellation to >> use. An alternative is aparc.a2009s which was developed by >> Christophe Destrieux. If this file is not found, it will exit >> with an error unless --skip in which case it skips this subject >> and moves on to the next. >> >> By default, the area (mm2) of each parcellation is reported. This can >> be changed with '--meas measure', where measure can be area, volume >> (ie, volume of gray matter), thickness, thicknessstd, or meancurv. >> thicknessstd is the standard dev of thickness across space. >> >> Example: >> aparcstats2table --hemi lh --subjects 004 008 --parc aparc.a2009s >> --meas meancurv -t lh.a2009s.meancurv.txt >> >> lh.a2009s.meancurv.txt will have 3 rows: (1) 'header' with the name >> of each structure, (2) mean curvature for each structure for subject >> >> The --common-parcs flag writes only the ROIs which are common to all >> the subjects. Default behavior is it puts 0.0 in the measure of an ROI >> which is not present in a subject. >> >> The --parcs-from-file <file> outputs only the parcs specified in the file >> The order of the parcs in the file is maintained. Specify one parcellation >> per line. >> >> The --report-rois flag, for each subject, gives what ROIs that are present >> in atleast one other subject is absent in current subject and also gives >> what ROIs are unique to the current subject. >> >> The --transpose flag writes the transpose of the table. >> This might be a useful way to see the table when the number of subjects is >> relatively less than the number of ROIs. >> >> The --delimiter option controls what character comes between the measures >> in the table. Valid options are 'tab' ( default), 'space', 'comma' and >> 'semicolon'. >> >> The --skip option skips if it can't find a .stats file. Default behavior >> is >> exit the program. >> >> The --parcid-only flag writes only the ROIs name in the 1st row 1st column >> of the table. Default is hemi_ROI_measure >> >> >> >> On Tue, Sep 3, 2013 at 11:08 AM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>>> >> wrote: >> >> Hi Alan, it would be a lot easier to help if you told us what the >> error >> msg is:). Please supply the full terminal output including error msg. >> thanks >> doug >> >> >> On 09/03/2013 10:52 AM, Alan Francis wrote: >> > Hi FreeSurfer folks: >> > >> > I am trying to extract LGI values from Brodmann Areas 44 and 45. >> I am >> > using the following script. Unfortunately it gives me an error >> > message. Could you please help me. >> > >> > aparcstats2table --skip -s /HM0403 /HM0503 /HM0603 /HM0703 /HM0903 >> > /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 >> > /HM2103 /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 >> > /HM3103 /HM3202 /HM3203 /HM3303 /HM3403 /HM3503 /HM3603 /HM3703 >> > /HM3903 /HM4003 /HM4203 /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 >> > /HM4803 /HM4903 /HM5103 /HM5203 /HM5303 /HM5403 /HM5503 /HM5603 >> > /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 /HM6303 /HM6403 /HM6503 >> > /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 /HM7203 /HM7303 >> > /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 /HM8203 >> > /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 >> --hemi >> > lh --parc=BA --meas foldind --tablefile BA44 BA45 -lh.BA.stats >> > --subjectsfile=BA_LGI.txt >> > >> > >> > thanks so much, >> > >> > Alan Francis >> > >> > >> > ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> > >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> Outgoing: >> >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.** >> harvard.edu <Freesurfer@nmr.mgh.harvard.edu>> >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. >> >> >> > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >
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