Try running it without --cortex
On 6/26/19 4:57 PM, Jennifer Legault wrote:
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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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