Try running it without --cortex

On 6/26/19 4:57 PM, Jennifer Legault wrote:
>
>         External Email - Use Caution
>
> Hi Freesurfer experts,
>
> I'm trying to constrain my sMRI analysis to only search for brain
> regions (GMV) that are correlated with a behavioral measure within a
> mask (made from a functional contrast of interest, so that I'm only
> searching for regions that were shown to be active during a language
> localizer task) using mri_glmfit.  I've followed recommended steps to
> transforming my fMRI contrast into a surface mask, and then later even
> tried making it into a surface label, however whenever I run the
> analysis, I get the same results regardless of whether I use the
> --mask or --label option, meaning that the summary file
> (cache.th40.pos.sig.cluster.summary) includes regions that are outside
> the mask.  How can I ensure that mri_glmfit actually uses the mask? 
> I've included below the commands I have run.
>
> I previously ran mri_glmfit to search the whole brain for regions
> significantly correlated with behavioral measures using the following
> command:
> mri_glmfit --y fsgd_VSL_std_age_gender_TIV.volume.00B.mgh --fsgd
> fsgd_VSL_std_age_gender_TIV.txt --C Contrast_VSL_std_a_g_TIV.txt
> --surf fsaverage lh --cortex --glmdir lh.VSL_std_age_gender_TIV.glmdir
>
> Now, when I try to use the mask, I get the same results as above
> (significant result in regions outside of mask), using the following
> command:
> mri_glmfit --y fsgd_VSL_std_age_gender_TIV.volume.00B.mgh --mask
> localizer_mask.mgh --fsgd fsgd_VSL_std_age_gender_TIV.txt --C
> Contrast_VSL_std_a_g_TIV.txt --surf fsaverage lh --cortex --glmdir
> lh.VSL_std_age_gender_TIV_localizer_mask.glmdir
>
> I also converted the mask into a label just in case, and used the
> following command:
> mri_glmfit --y fsgd_VSL_std_age_gender_TIV.volume.00B.mgh --label
> <path>/freesurfer/fsaverage/label/LeftMidAntTemp_surf.label --fsgd
> fsgd_VSL_std_age_gender_TIV.txt --C Contrast_VSL_std_a_g_TIV.txt
> --surf fsaverage lh --cortex --glmdir
> lh.VSL_std_age_gender_TIV_localizer_label.glmdir
>
> Across all these conditions, I always get the same results (even if
> the significant region is outside of the mask).  Are there any
> recommendations for steps I should take to make sure I'm only
> searching for regions inside the mask?
>
> Best,
>
> Jen
> --
>
> Jennifer Legault
> PhD, Neuroscience
> Postdoctoral Scholar
> Language Acquisition and Brain Lab
> University of Delaware
>
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