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

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