On 02/03/2016 08:20 AM, Bittner, Nora wrote:
Dear FreeSurfer Experts,
I have two questions, which you can hopefully answer to:
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 regrettably http://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?
It should be --vox, not --crs. And don't include "vertexno", just use the 3 numbers.
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?
You can again use mri_segstats,passing it --annot to get a table of effect sizes averaged over each aparc annotation. Run mri_segstats with --help to get more info
Thank you in advance,
Nora Bittner
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