Dear FreeSurfer experts,
I did a group analysis in QDEC for the symmetric percent change from pre to post and have a couple of clusters that don't survive the Monte Carlo correction. I want to extract the values for each time point per subject for those clusters that are bigger than 150 vertices to look at individual trends. How could I achieve this?
Thank you for your help. Clara
----- Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany
Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn@cbs.mpg.de
You can run mri_surfcluster using the sig.mgh as the input and specifying a --minarea and --thmin .001. --minarea takes a surface area in mm2, not number of vertices, so you'll have to compute what the approx area is of 150 vertices. Include a --ocn output and --sum sumfile, then use mri_segstats with --seg ocn.mgh --excludeid 0 --i y.mgh --avgwf y.sum.dat
The output y.sum.dat will be a matrix of number of subjects by number of clusters. Look in the sumfile for the cluster identity
On 02/01/2017 11:41 AM, Clara Kühn wrote:
Dear FreeSurfer experts,
I did a group analysis in QDEC for the symmetric percent change from pre to post and have a couple of clusters that don't survive the Monte Carlo correction. I want to extract the values for each time point per subject for those clusters that are bigger than 150 vertices to look at individual trends. How could I achieve this?
Thank you for your help. Clara
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany
Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn@cbs.mpg.de
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
thanks for your reply. I'm trying it out but I get this error message: ERROR: srcsubjid must be supplied
I have 40 subjects in 2 groups. What exactly do I enter as --subject ?
Thanks for your help! Clara
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 1. Februar 2017 19:18:55 Betreff: Re: [Freesurfer] extract values uncorrected clusters
You can run mri_surfcluster using the sig.mgh as the input and specifying a --minarea and --thmin .001. --minarea takes a surface area in mm2, not number of vertices, so you'll have to compute what the approx area is of 150 vertices. Include a --ocn output and --sum sumfile, then use mri_segstats with --seg ocn.mgh --excludeid 0 --i y.mgh --avgwf y.sum.dat
The output y.sum.dat will be a matrix of number of subjects by number of clusters. Look in the sumfile for the cluster identity
On 02/01/2017 11:41 AM, Clara Kühn wrote:
Dear FreeSurfer experts,
I did a group analysis in QDEC for the symmetric percent change from pre to post and have a couple of clusters that don't survive the Monte Carlo correction. I want to extract the values for each time point per subject for those clusters that are bigger than 150 vertices to look at individual trends. How could I achieve this?
Thank you for your help. Clara
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany
Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn@cbs.mpg.de
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
fsaverage
On 02/03/2017 06:04 AM, Clara Kühn wrote:
Hi Doug,
thanks for your reply. I'm trying it out but I get this error message: ERROR: srcsubjid must be supplied
I have 40 subjects in 2 groups. What exactly do I enter as --subject ?
Thanks for your help! Clara
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 1. Februar 2017 19:18:55 Betreff: Re: [Freesurfer] extract values uncorrected clusters
You can run mri_surfcluster using the sig.mgh as the input and specifying a --minarea and --thmin .001. --minarea takes a surface area in mm2, not number of vertices, so you'll have to compute what the approx area is of 150 vertices. Include a --ocn output and --sum sumfile, then use mri_segstats with --seg ocn.mgh --excludeid 0 --i y.mgh --avgwf y.sum.dat
The output y.sum.dat will be a matrix of number of subjects by number of clusters. Look in the sumfile for the cluster identity
On 02/01/2017 11:41 AM, Clara Kühn wrote:
Dear FreeSurfer experts,
I did a group analysis in QDEC for the symmetric percent change from pre to post and have a couple of clusters that don't survive the Monte Carlo correction. I want to extract the values for each time point per subject for those clusters that are bigger than 150 vertices to look at individual trends. How could I achieve this?
Thank you for your help. Clara
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany
Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn@cbs.mpg.de
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Clara Kühn -
Douglas N Greve