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Hi Doug,
Ok, that's fine. Is it possible to visualize subcortical volume differences in any way?
Thank you! Julia
NIHR Maudsley Biomedical Research Centre PhD Student Forensic & Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience King's College London 16 De Crespigny Park, Camberwell London, SE5 8AB
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: 16 April 2021 16:11 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] glmfit with aseg table: view surface overlay
Are you trying to correct the table? You can't do that with mri_gtlmfit-sim. That looks for clusters, which does not make sense when you are using table data. There are a couple of ways you can do it. One is with bonerfonni correction (ie, multiply the p-value by the number of ROIs) or with FDR. On 4/15/2021 11:13 AM, Griem, Julia wrote:
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External Email - Use Caution Hi Doug,
Thank you. Makes sense. Is there any way to visualize significance overlays for the subcortical volumes?
I've also moved on to the correction for multiple comparisons in my subcortical volumes, using:
mri_glmfit-sim -- glmdir roi.binarygroup.glmdir --perm 1000 1.3 abs --cwp 0.05 --2spaces --bg 1
This did not create any new files in the Contrast subdirectories, but the log file does say that it was run and finished. Can I find a table with corrected p-values anywhere? Or would it make more sense to move the aseg_table into a different stats package and calculate my GLM there, correcting for multiple comparisons post-hoc (manually)?
Thank you so much Julia
NIHR Maudsley Biomedical Research Centre PhD Student Forensic & Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience King's College London 16 De Crespigny Park, Camberwell London, SE5 8AB
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: 15 April 2021 15:14 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] glmfit with aseg table: view surface overlay
The input is a table, so the output is a table (the sig.mgh file will just have the number of values that are in the table; this is not a "volume" you can look at in FV). Look in the sig.table.dat file for the sigs. On 4/13/2021 8:41 AM, Griem, Julia wrote:
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External Email - Use Caution Dear Freesurfer team,
I am comparing subcortical volumes (aseg table) in 2 groups with no other variables. Based on the GLM lecture slides from the course I attended, I ran the following glmfit command: mri_glmfit --table aseg_table.txt --fsgd FSGD/DemographicsSubcortBinaryGroup.fsgd --C Contrasts/HC-ASPD.mtx --C Contrasts/ASPD-HC.mtx --glmdir roi.binarygroup.glmdir
It created all the correct output and subdirectories.
I then used freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=ASPD-HC/sig.mgh
but an error saying "failed to load surface overlay" comes up and the terminal error message is "number of vertices in overlay data does not match with surface". I assume this is because I am trying to load a 'whole-brain' sig.mgh onto a lh surface? Do I have to change the glmfit command to specify hemispheres, and if so, how do I do that since I do not want to look at cortical but subcortical data? Or alternatively, can I load both hemispheres into freeview so the overlay sig.mgh fits?
Thank you so much, Julia
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