Can you include the full command line (no $variables) and the full
terminal output?

On 1/2/19 4:22 PM, Tamara Sussman wrote:
>
>         External Email - Use Caution
>
> 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
> <mailto:ts%2Bml@rcmd.org>> wrote:
>
>           External Email - Use Caution
>
>     What are $label and $input set to?
>
>     > On January 2, 2019 at 9:13 PM Tamara Sussman <tsussman@gmail.com
>     <mailto:tsussman@gmail.com>> wrote:
>     >
>     >
>     >         External Email - Use Caution
>     >
>     > 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
>     > _______________________________________________
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>     --
>     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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