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-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 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 atsiknia@health.ucsd.edu mailto:atsiknia@health.ucsd.edu

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1B8ZgScqX_2ARIhaIvy7DRe6zOoOpBMp5-dXi7r4k0YgdEmbWyoSruaJ-YGhyiA2RYRDhf-5G7Rze-mKVSKUQYSgImHwmSMsClPiKynVJnMAjOL_-cRRsyChq_cHHDnQS_d5UUciZQLSJlw40IIAocAkyJc5xRRuvKNzkWp-DVFeatl54RKDsa39xaUGth7w5h2WU0ZNdX3f7S9eUANEZGZYddpyCjgdq826FCtrivPMbT47KvGjR9p34Cu9NdwG1eTalWnG2Sejmpiijg1bU0g/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__%3B%21%21LLK065n_VXAQ%210X2hfmq1jpXVRbMUKok52G_OBRwfGRKSFLyDalF69Wjj5BP_2itlWyZkdP3VLsilyA%24

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer