Re: [Freesurfer] mask error in glm_fit

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Thanks for your response! It was in the fsaverage folder when I installed Freesurfer. I also have an .nii file. Could I turn it into an .mgz file and maybe it will have the same dimensions? Could it also be because I am looking at volume and fsaverage is(?) a surface thing?

Haley

On Mon, May 10, 2021 at 11:15 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:

It is saying that the mask lhYeo2011_7NetworksConfidence_N1000.mgz does not have thee same dimensions as the input. How was it created? It must be a surface overlay on fsaverage

On 4/26/2021 6:59 PM, Haley Park wrote:

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Hello,

I am trying to run a correlational analysis with glm_fit on a masked area with the code:

foreach hemi (lh)

foreach smoothness (10)

foreach meas (volume thickness)

    mri_glmfit \

    --y {$hemi}.{$meas}.{$study}.{$smoothness}.mgh \

    --fsgd FSGD/{$study}.fsgd \

    --C Contrasts/Scores_Slope.mtx  \

    --surf fsaverage {$hemi}  \

    --mask lhYeo2011_7NetworksConfidence_N1000.mgz  \

    --glmdir {$hemi}.{$meas}.{$study}.{$smoothness}.glmdir

end

end

end

I get the error message:

ERROR: dimension mismatch 1 between y and mask

I've also tried to run it with the .nii file found at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1UZFGqmdxRuc0MnBvkd8bVFBWOYwZRCwO0HZNjVOvoumBUi... https://secure-web.cisco.com/1sTopz8rXlJoh4VSQL7P0DYm1ff7H5Crs0Qg3iAG1M6HD6Vuyjn8ViA2fDeX0A7VIH_9-GSxTfaL35eIjCKAnbUd90wxlxBlgtdz3DVFpnalWP2oV1jHapx5B4tlAXHpUA9N18syK8T_8U3eUIX2YC8P7r4l3verT5XzzxpTkHDB7Nmuh-RYY63YVpXWmTl_xCbs105PDuuWwbrTX5RfdknvxXBksPePKuZnNwqmGz-GLy8z8xYTDCYxHegxv5wG_XMQjD1PxSwhpaqG0N-mGvQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FCorticalParcellation_Yeo2011

Any help would be appreciated!

Haley

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