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:
Specify each subject after a -s flag
-s subject1 -s subject2 ... --hemi lhSpecify all subjects after --subjects flag. --subjects does not have to be the last argument. Eg:
--subjects subject1 subject2 ... --hemi lhBy 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 <greve@nmr.mgh.harvard.edu mailto:greve@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: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 <mailto:greve@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> FileDrop: 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.