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.
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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MGH-NMR Center
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