Hi,

I am running glmfit on some functional data (using ces.nii.gz surface files as input) using ROIs and the --mask argument, that I plan to later submit to glmfit-sim for small volume correction.  I have some rois that are subcortical and some that are surfaces.  For the glmfit run within the surface ROIs the output sig.nii.gz files all voxels have a value of zero. However, this is not the case for the F.nii.gz and z.nii.gz files output by the same glmfit command - they have non-zero voxels. This issue only occurs for the surface ROIs, when I run glmfit in subcortical ROIs the sig.nii.gz files look normal.

The surface ROIs were created by using afnis 3dundump to create 10mm spheres from MNI coordinates. I then ran the MNI template through freesurfer, and used the regheader from this to run mri_vol2surf to put the spherical ROIs into fsaverage space.  I am able to view the resulting surface ROIs projected onto the fsaverage surface in freeview, and have checked that my ces.nii.gz function files can also be overlayed onto the same fsaverage template in freeview.

The output of one of the glmfit commands in question is below.

thanks!

WARNING: gdfReadV1: no variables on 'Variables' line found

Reading source surface /autofs/cluster/neuromod/programs/freesurfer_7.1.1/freesurfer/subjects/fsaverage/surf/lh.white

gdfRead(): reading /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/inputFiles/

/fsgd.txt

INFO: gd2mtx_method is dods

Number of vertices 163842

Number of faces    327680

Total area         65417.000000

AvgVtxArea       0.399269

AvgVtxDist       0.721953

StdVtxDist       0.195472

7.1.1

cwd /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast

cmdline mri_glmfit --glmdir /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lC

S+E_m_lCS-atCS+E/outputFiles/lIFG/ --y /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recal

l//recall.sm5.lh/lCS+E_m_lCS-atCS+E/ces.nii.gz --surf fsaverage lh --fsgd /autofs/space/uriline_003/users/projects/OC

D_NM/walker_pedersen/data/image/main/recall/inputFiles//fsgd.txt --C /autofs/space/uriline_003/users/projects/OCD_NM/

walker_pedersen/data/image/main/recall/inputFiles//groupDiff.mtx --nii.gz --mask /autofs/cluster/neuromod/NIFTI/OCD_N

M/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz --eres-save

sysname  Linux

hostname r440-28.nmr.mgh.harvard.edu

machine  x86_64

user     wsp6

FixVertexAreaFlag = 1

UseMaskWithSmoothing     1

OneSampleGroupMean 0

y    /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recall/recall.sm5.lh/lCS+E_m_lCS-atCS+E

/ces.nii.gz

logyflag 0

usedti  0

FSGD /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/inputFiles//fsgd.txt

mask /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz

maskinv 0

glmdir /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_m_lCS-atCS+E/outp

utFiles/lIFG/

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+

E_m_lCS-atCS+E/outputFiles/lIFG/

Loading y from /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recall/recall.sm5.lh/lCS+E_m_

lCS-atCS+E/ces.nii.gz

   ... done reading.

INFO: gd2mtx_method is dods

Saving design matrix to /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_

m_lCS-atCS+E/outputFiles/lIFG//Xg.dat

Computing normalized matrix

Normalized matrix condition is 1

Matrix condition is 1.125

Pruning voxels by thr: 1.175494e-38

Found 512 voxels in mask

Saving mask to /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_m_lCS-atC

S+E/outputFiles/lIFG//mask.nii.gz

Reshaping mriglm->mask...

search space = 222.026773

DOF = 15

Starting fit and test

Fit completed in 0.0002 minutes

Computing spatial AR1 on surface

Residual: ar1mn=0.987586, ar1std=0.043927, gstd=3.620916, fwhm=8.526606

Writing results

  groupDiff

MRImask(): AllowDiffGeom = 1

INFO: MRImask() using MRImaskDifferentGeometry()

    maxvox sig=-0  F=4.36504  at  index 391 0 0    seed=1632900996

mri_glmfit done

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