Dear FS experts
We would like to correlate the cortical thickness of a particular vertex or the mean thickness of a region with the thickness of all other vertices in one hemisphere. Therefore my question:
Is there any tool in FS yet that is able to do that?
Thanks in advance Best regards Juergen
----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------
Hello everybody,
It's some time ago that I did some group analyses for cortical thickness and after glancing through the new documentation I believe (or hope) that I still know how do do a group comparison (e.g. patients vs controls).
I have, however, never tried analyses of groups at different time points. I assume this a quite obvious problem many people have been working with and I will find more about when I really read the documentation but I hope that somebody could hint me where to look. So, I have patients who have been scanned a couple of years ago and, once again, just recently and I want to do what you would expect:
1. Just look for an individual subject whether cortical thinning is more prominent in some regions compared to others 2. Run paired tests for the cortical thickness where the pairs obviously are the data sets of the same subject at different time points.
Most likely many people have done the very same thing with freesurfer, so anybody willing to discuss the way to do it and potential pitfalls?
Thanks in advance
Claus
----------------------------------------------------------------------- Claus Tempelmann email: Claus.Tempelmann@medizin.uni-magdeburg.de Clinic for Neurology II MR department Tel.: +49-(0)391-6117183 OvG University Magdeburg +49-(0)391-6117177 Leipziger Strasse 44 39120 Magdeburg Fax: +49-(0)391-6117178 Germany
Hi Claus,
the easiest way to do a paired t test is to run mris_preproc with the --paired-diff option. Make sure to specify time point 1 and 2 for each subject sequentially. You can do a stat test on each individual with only 2 time points.
doug
On Fri, 22 Feb 2008, Claus Tempelmann wrote:
Hello everybody,
It's some time ago that I did some group analyses for cortical thickness and after glancing through the new documentation I believe (or hope) that I still know how do do a group comparison (e.g. patients vs controls).
I have, however, never tried analyses of groups at different time points. I assume this a quite obvious problem many people have been working with and I will find more about when I really read the documentation but I hope that somebody could hint me where to look. So, I have patients who have been scanned a couple of years ago and, once again, just recently and I want to do what you would expect:
- Just look for an individual subject whether cortical thinning is
more prominent in some regions compared to others 2. Run paired tests for the cortical thickness where the pairs obviously are the data sets of the same subject at different time points.
Most likely many people have done the very same thing with freesurfer, so anybody willing to discuss the way to do it and potential pitfalls?
Thanks in advance
Claus
Claus Tempelmann email: Claus.Tempelmann@medizin.uni-magdeburg.de Clinic for Neurology II MR department Tel.: +49-(0)391-6117183 OvG University Magdeburg +49-(0)391-6117177 Leipziger Strasse 44 39120 Magdeburg Fax: +49-(0)391-6117178 Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Claus,
One approach to do a direct thickness comparison, as was done for a test-retest study described here:
https://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility
There's a link on this page to the paper that was published.
That might be all you need. It is also possible to use mri_glmfit (or qdec) to do a group analysis.
Nick
On Fri, 2008-02-22 at 15:27 +0100, Claus Tempelmann wrote:
Hello everybody,
It's some time ago that I did some group analyses for cortical thickness and after glancing through the new documentation I believe (or hope) that I still know how do do a group comparison (e.g. patients vs controls).
I have, however, never tried analyses of groups at different time points. I assume this a quite obvious problem many people have been working with and I will find more about when I really read the documentation but I hope that somebody could hint me where to look. So, I have patients who have been scanned a couple of years ago and, once again, just recently and I want to do what you would expect:
- Just look for an individual subject whether cortical thinning is
more prominent in some regions compared to others 2. Run paired tests for the cortical thickness where the pairs obviously are the data sets of the same subject at different time points.
Most likely many people have done the very same thing with freesurfer, so anybody willing to discuss the way to do it and potential pitfalls?
Thanks in advance
Claus
Claus Tempelmann email: Claus.Tempelmann@medizin.uni-magdeburg.de Clinic for Neurology II MR department Tel.: +49-(0)391-6117183 OvG University Magdeburg +49-(0)391-6117177 Leipziger Strasse 44 39120 Magdeburg Fax: +49-(0)391-6117178 Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Juergen,
qdec will certainly do this on a parcel basis. I'll leave the correlation map for Doug.
cheers, Bruce On Fri, 22 Feb 2008, Juergen Haenggi wrote:
Dear FS experts
We would like to correlate the cortical thickness of a particular vertex or the mean thickness of a region with the thickness of all other vertices in one hemisphere. Therefore my question:
Is there any tool in FS yet that is able to do that?
Thanks in advance Best regards Juergen
Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You can add the value you want as a continuous variable in an fsgd file, then set up a contrast to test it.
On Fri, 22 Feb 2008, Juergen Haenggi wrote:
Dear FS experts
We would like to correlate the cortical thickness of a particular vertex or the mean thickness of a region with the thickness of all other vertices in one hemisphere. Therefore my question:
Is there any tool in FS yet that is able to do that?
Thanks in advance Best regards Juergen
Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Claus Tempelmann -
Doug Greve -
Juergen Haenggi -
Nick Schmansky