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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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:*[email protected]
<[email protected]> *On Behalf Of *Douglas N. Greve
*Sent:* 15 April 2021 15:14
*To:* [email protected]
*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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