Hi Gayane, I don't know whether I answered this or not, but you will need to add "--surface fsaverage lh" to your command line doug
On 06/24/2013 12:18 PM, Gayane Aghakhanyan wrote: > Dear FreeSurfers > > I'm using Freesurfer 5.1 on Ubuntu 12.04 LTS. > Currently running paired analysis as described here > https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis > > After > mri_glmfit \ > --glmdir lh.paired-diff \ > --y lh.paired-diff.thickness.sm05.mgh \ > --fsgd paired-diff.fsgd \ > --C mean.mtx \ > --C age.mtx > > I've got an error "ERROR: you must use '--surface subject hemi' with surface > data". > Any idea how to fix it? > > Below is the full output: > > utente@RM-user:~/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis$ > mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh > --fsgd paired-diff.fsgd --C mean.mtx --C age.mtx > > > gdfReadHeader: reading paired-diff.fsgd > INFO: ignoring tag ,9 > INFO: ignoring tag ,9 > INFO: ignoring tag ,3 > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. > Continuous Variable Means (all subjects) > > > 0 Age 57 11.0454 > Class Means of each Continuous Variable > 1 Main 57.0000 > INFO: gd2mtx_method is dods > > $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ > cwd > /home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis > > > cmdline mri_glmfit --glmdir lh.paired-diff --y > lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx --C > age.mtx > sysname Linux > hostname RM-user > machine x86_64 > user utente > FixVertexAreaFlag = 1 > > > UseMaskWithSmoothing 1 > OneSampleGroupMean 0 > y > /home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis/lh.paired-diff.thickness.sm05.mgh > logyflag 0 > usedti 0 > > FSGD paired-diff.fsgd > > glmdir lh.paired-diff > IllCondOK 0 > ReScaleX 1 > DoFFx 0 > Creating output directory lh.paired-diff > Loading y from > /home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis/lh.paired-diff.thickness.sm05.mgh > > > ERROR: you must use '--surface subject hemi' with surface data > > Thanks for yuo help > Gayane > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 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.
