Dear FreeSurfer Experts,
Sorry for reposting this massage again, but I still 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. Now, I would like to extract these effect sizes in 'table' format. I tried to use mri-segstats:
mri_segstats* --i effectsize.mgh --annot fsaverage lh aparc --avgwf effectsize.dat
I am not sure, if this gives me the correct results. Is this the right command? I would really appreciatehttp://dict.leo.org/ende/index_en.html#/search=appreciate&searchLoc=0&resultOrder=basic&multiwordShowSingle=on your help.
Thank you in advance, Nora
------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
On 02/29/2016 02:38 AM, Bittner, Nora wrote:
Dear FreeSurfer Experts,
Sorry for reposting this massage again, but I still 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?
Remember, you can always run commands with --help to get more info. If you run this command with --help, you will see: --vox C R S replace seg with all 0s except at CRS
So use --vox, not --crs.
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. Now, I would like to extract these effect sizes in 'table' format. I tried to use mri-segstats:
mri_segstats* --i effectsize.mgh --annot fsaverage lh aparc --avgwf effectsize.dat
I am not sure, if this gives me the correct results. Is this the right command?
I would really appreciate http://dict.leo.org/ende/index_en.html#/search=appreciate&searchLoc=0&resultOrder=basic&multiwordShowSingle=on your help.
Yes, that will give you the effect size averaged over each annotation
Thank you in advance,
Nora
Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Bittner, Nora -
Douglas N Greve