Do you see the note: "make sure at least one voxel has a non-zero value
for each input"? To do this, you can try loading the input into
freeview, eg,
tksurferfv fsaverage lh inflated -ov h.N0s2_e4pos.10.mgh -fminmax .0001 1
It will come up with a map of the first subject. Scroll through the
subjects using the "frame" button. Look for one or more subjects where
the values are 0 across the surface
On 9/15/2021 4:50 PM, Tsiknia, Amaryllis wrote:
External Email - Use Caution
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
sysnameLinux
hostname ip27.ucsd.edu
machinex86_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
usedti0
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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 thetext 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
atsik...@health.ucsd.edu <mailto:atsik...@health.ucsd.edu>
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