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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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