Sorry Prapti, I was confused, the exact commands are: mris_anatomical_stats -a aparc.annot -t pial_lgi -f #SUBJ/stats/ lh.aparc_lgi.stats #SUBJ lh
and then aparcstats2table --subjects #SUBJ1 #SUBJ2 ... --hemi lh --meas thickness --parc aparc_lgi --t YOUR_OUTPUT_TABLE Hope it will work, Marie On 17 nov. 10, at 02:44, Prapti Gautam wrote: > > > Hi Marie, > > I've done what was suggested but I've encountered a problem. I will > recount my steps: > > I used mri_anatomical_stats to create a file called lh.lgi.stats in > the label directory of subjects. I've double checked to see that the > file indeed contains lgi values and not thickness values (they are > different values from a separately tabulated files for thickness) > > next I'm trying to pass this file as the input to the > aparcstats2table with the command you specified. The syntax I ran is: > > > aparcstats2table --hemi lh --subject test --measure thickness -- > tablefile test/label/lh.lgi.stats -t lh.lgi.table > > My output is now saved in the file lh.lgi.table, but it contains > thickness values instead of lgi values from the tablefile. Can you > please tell me what I am missing here? > > thank you, > > Prapti > > -----Original Message----- > From: Marie Schaer [mailto:marie.sch...@unige.ch] > Sent: Wed 11/17/2010 12:39 AM > To: Prapti Gautam > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Mean lGI value extraction > > Hi Prapti, > > Normally you can use aparcstats2table exactly as you would do with > thickness, given that the column corresponding to thickness values in > the tablefile that you produced with your mris_anatomical_stats are > indeed lgi values (i.e. you used mris_anatomical_stats -t pial_lgi -f > lh.lgi.stats, which allows you to use: aparcstats2table -- > subjects ...... --hemi ?h --measure thickness --tablefile ? > h.lgi.stats). > > Let me know if you encounter any problem, > > Marie > > > On 16 nov. 10, at 04:28, Prapti Gautam wrote: > >> dear all, >> >> I am trying to extract the mean values of lgi from the cortex from a >> group of subjects. I found the following command useful in >> extracting for one subject: >> >> mris_anatomical_stats -mgz -f lh.lgi.stats -b -a aparc.annot -c >> lh.lgi.annot.ctab -t pial_lgi $SUBJECT lh >> >> However, I have a lot of subjects I wish to extract this for and I >> was wondering if there is a command that will extract these values >> similar to the aparcstats2table command (where all the subjects and >> the mean values for each parcellation is in one output file) >> >> thanks, >> >> Prapti >> >> _______________________________________________ >> 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
