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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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you, that worked perfectly!
Best,
Jen
On Wed, Jun 26, 2019 at 5:27 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Try running it without --cortex
On 6/26/19 4:57 PM, Jennifer Legault wrote:
External Email - Use CautionHi 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Greve, Douglas N.,Ph.D. -
Jennifer Legault