The first command does not work because --slabel requires three options and it is interpreting "--i" and "/Volumes...mgh" as those two so it thinks you have not included. It is probably better to use something like mri_segstats --seg ocn.mgh --excludeid 0 --avgwf test.dat --sumTest_SupParietal.sum --i lh.thickness.fwhm10.fsaverage.mgh
On 1/3/19 2:41 PM, Tamara Sussman wrote: > > External Email - Use Caution > > Thanks so much for your suggestion, Douglas. > Here is the whole input and output: > > Tamara-Posner-lab:~ posnerlab$ mri_segstats --slabel > /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label > > --i/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/surf/lh.thickness.fwhm10.fsaverage.mgh > > --nonempty --excludeid 0 --avgwf test.dat --sumTest_SupParietal.sum > > ERROR: cannot do frame average without input volume > > > I was using --slabel instead of --seg because I am using surfaces, and > not volumes. Just to test it out, I tried using the --seg aseg too, > and got the same error: > > Tamara-Posner-lab:~ posnerlab$ mri_segstats --seg > /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/mri/aseg.mgz > > --mask > /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label > > --nonempty --excludeid 0 --avgwf test.dat --sumTest_SupParietal.sum > > ERROR: cannot do frame average without input volume > > Thank you again for your help! > Tamara > > > On Thu, Jan 3, 2019 at 1:59 PM Greve, Douglas N.,Ph.D. > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > 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...@rcmd.org > <mailto:ts%2...@rcmd.org> > > <mailto:ts%2...@rcmd.org <mailto:ts%252...@rcmd.org>>> wrote: > > > > External Email - Use Caution > > > > What are $label and $input set to? > > > > > On January 2, 2019 at 9:13 PM Tamara Sussman > <tsuss...@gmail.com <mailto:tsuss...@gmail.com> > > <mailto:tsuss...@gmail.com <mailto:tsuss...@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> > > <mailto: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> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
