I can't tell from the glmfit command line what you are trying to do. Generally, the GLM is run on group data and you specify an average brain (eg, fsaverage) as the --surf.

On 07/14/2016 06:10 AM, Chatzi, Vasiliki wrote:

Dear Developers,

I am trying to run the mri_glmfit command and I get two different errors for two different subjects. Please find details below. I would be really grateful if you could provide any advice.

Error1

setenv SUBJECTS_DIR ./

mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt --no-contrasts-ok --surf subject1 lh

gdfReadHeader: reading fsgd_test2.txt

INFO: gd2mtx_method is dods

Reading source surface .//subject1/surf/lh.white

Number of vertices 167703

Number of faces 335402

Total area 108706.031250

AvgVtxArea 0.648206

AvgVtxDist 0.881642

StdVtxDist 0.250483

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $

cwd /home/test

cmdline mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt --no-contrasts-ok --surf subject1 lh

sysname Linux

hostname

machine x86_64

user

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y /home/test/lh.10.lgi.mgh

logyflag 0

usedti 0

FSGD fsgd_test2.txt

labelmask .//subject1ii/label/lh.cortex.label

maskinv 0

glmdir ./

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory ./

Loading y from /home/test/lh.10.lgi.mgh

INFO: gd2mtx_method is dods

Saving design matrix to .//Xg.dat

Normalized matrix condition is 1

Matrix condition is 1

Found 158404 points in label.

ERROR: mri_reshape: number of elements cannot change

nv1 = 167703, nv1 = 163842

Pruning voxels by thr: 0.000000

Found 163842 voxels in mask

Saving mask to .//mask.mgh

Reshaping mriglm->mask...

ERROR: mri_reshape: number of elements cannot change

nv1 = 163842, nv1 = 167703

search space = 108705.102552

DOF = 0

ERROR: DOF = 0

Error 2 setenv SUBJECTS_DIR ./ mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt --no-contrasts-ok --surf subject2 lh gdfReadHeader: reading fsgd_test2.txt INFO: gd2mtx_method is dods Reading source surface .//subject2/surf/lh.white Number of vertices 129318 Number of faces 258632 Total area 86174.742188 AvgVtxArea 0.666379 AvgVtxDist 0.893985 StdVtxDist 0.260921 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /home/test cmdline mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt --no-contrasts-ok --surf subject2 lh sysname Linux hostname machine x86_64 user FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/test/lh.10.lgi.mgh logyflag 0 usedti 0 FSGD fsgd_test2.txt labelmask .//subject2/label/lh.cortex.label maskinv 0 glmdir ./ IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory ./ Loading y from /home/test/lh.10.lgi.mgh INFO: gd2mtx_method is dods Saving design matrix to .//Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 121215 points in label. ERROR: mri_reshape: number of elements cannot change nv1 = 129318, nv1 = 163842 Pruning voxels by thr: 0.000000 Segmentation fault

Bets wishes, Vasiliki

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