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Sorry about that! Here's the full terminal output: 

cwd /space/syn01/1/data/MMILDB/MCE_RBS/fsurf

cmdline mri_glmfit.bin --y lh.N0s2_e4pos.10.mgh --fsgd ./fsgd_omega/e4_positive.fsgd dods --C ./mtx_omega/e4_positive.mtx --surf fsaverage lh --cortex --glmdir lh.N0s2_e4pos.glmdir 

sysname  Linux

hostname ip27.ucsd.edu

machine  x86_64

user     mmilrec5

FixVertexAreaFlag = 1

UseMaskWithSmoothing     1

OneSampleGroupMean 0

y    /space/syn01/1/data/MMILDB/MCE_RBS/fsurf/lh.N0s2_e4pos.10.mgh

logyflag 0

usedti  0

FSGD ./fsgd_omega/e4_positive.fsgd

labelmask  /usr/pubsw/packages/freesurfer/RH4-x86_64-R600/subjects/fsaverage/label/lh.cortex.label

maskinv 0

glmdir lh.N0s2_e4pos.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory lh.N0s2_e4pos.glmdir

Loading y from /space/syn01/1/data/MMILDB/MCE_RBS/fsurf/lh.N0s2_e4pos.10.mgh

   ... done reading.

INFO: gd2mtx_method is dods

Saving design matrix to lh.N0s2_e4pos.glmdir/Xg.dat

Computing normalized matrix

Normalized matrix condition is 13.691

Matrix condition is 98.2187

Found 149955 points in label.

Pruning voxels by thr: 1.175494e-38

Found 0 voxels in mask

ERROR: no voxels found in the mask

  make sure at least one voxel has a non-zero value for each input


From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Wednesday, September 15, 2021 1:19 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_glmfit 0 voxels in mask ERROR
 
Can't see the image. Can you just cut-and-paste the full terminal output into the email?

On 9/15/2021 3:02 PM, Tsiknia, Amaryllis wrote:

        External Email - Use Caution        

Dear Freesurfer Team, 

I have been struggling with an error using the mri_gmfit command. I have been trying to run a simple surface-based group analysis on 28 subjects testing whether a continuous variable "OMEGA3_457" relates to various RSI measures while adjusting for the effects of gender. 

This is the error I am getting:

Image preview

and attached is my .fsgd file. The matrix file I am using is testing for the following contrast: 0 0 0.5 0.5. 

I produced the lh.N0s2_e4pos.10.mgh file using the mri_surf2surf command after using mri_concat to concatenate the RSI data for all 28 of our subjects into a single lh.N0s2_e4pos.00.mgh file. I have also attached the text file (containing all the paths to the subject data) that was fed into the mri_concat command.

Any help would be immensely appreciated. 

Thank you, 

Amaryllis A. Tsiknia 
Imaging Researcher
Department of Neurosciences 
University of California, San Diego
atsiknia@health.ucsd.edu


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