Re: [Freesurfer] Extracting cortical thickness from a significant cluster in an independent sample

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Thanks for your response - yes, I should have included this information before. :)

$label was set to a label I made by 1. binarizing the cluster results from the previous analysis, and then 2. using mri_vol2label to convert this into a label

label=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label

$input was set to an individual's thickness data (analogous data that I used in the initial analysis): input= /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/surf/lh.thickness.fwhm10.fsaverage.mgh

On Wed, Jan 2, 2019 at 4:09 PM ts+ml@rcmd.org wrote:

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What are $label and $input set to?

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On January 2, 2019 at 9:13 PM Tamara Sussman tsussman@gmail.com wrote:

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Hello Freesurfer Experts!

Thank you in advance for considering this question.

I did a cortical thickness analysis (surface-based), and found a significant cluster. I found the average cortical thickness in* this

group*,

...

in the .*y.ocn.dat* file, which is great.

Now I want to find the average cortical thickness in the same cluster,

in a

...

separate group of subjects.

I tried using mri_segstats, but it doesn't seem to work:

mri_segstats --slabel $label --i $input --nonempty --excludeid 0 --avgwf test.dat --sum Test_SupParietal.sum

The error I am getting is:

ERROR: cannot do frame average without input volume

Any thoughts about a better way to approach this analysis?

Thanks again in advance! -T _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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