Dear FreeSurfer Experts,
I have two questions, which you can hopefully answer to:
1) I calculated several analyses with LGI as my dependent variable, resulting in several significant clusters. Now, I would like to extract the individual LGI value at the maximum vertex of each significant cluster to plot it against my experimental variables (instead of working with the mean LGI values of the clusters). What I tried so far is to use mri_segstats to extract the LGI at the maximum vertex:
mri_segstats --i $SUBJECTS_DIR/qdec/glm/y.mgh --crs vertexno 84367 0 0 --avgwf vertexno84367.dat
where y.mgh is my input file from the glm and vertexno 84367 is the maximum vertex of the cluster as reported in the cluster.summary-file.
I found the command in the FS helpline documentation (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42655.html), but regrettablyhttp://dict.leo.org/ende/index_en.html#/search=regrettably&searchLoc=0&resultOrder=basic&multiwordShowSingle=on I get the following error message:
"ERROR: Option --crs unkown"
In the fswiki I also couldn´t find the "mri_segstats - - crs option" in the user description.
Is there any other option or argument I can use in mri_segstats (or in any other command) to extract the LGI value per person at the given vertex?
2) I would like to calculate effect sizes of my results. Therefore I used fscalc:
fscalc $SUBJECTS_DIR/qdec/glm/contrast/gamma.mgh div $SUBJECTS_DIR/qdec/glm/rstd.mgh -o $SUBJECTS_DIR/qdec/ glm/contrast/effectsize.mgh
This worked fine and resulted in a surface overlay displaying the effect sizes. Is there any way to convert this effectsize.mgh-file to a table format? Such that I would get numerical values, let´s say, vertexwise effect sizes or similar?
Thank you in advance, Nora Bittner
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