Dear list members!
I would like to analye cortical thickness data and wonder which is the best way to proceed...
So far I have processed the data using recon all (including manual top fixing). This includes the registration using the average7 subj. on the sphere.
1) Is it a valid approach to use the coreg. on the average7 or should I take a similar approach as used by VBM building a study specific template and do the coreg step on this template once again.
2) For doing the cortical thickness group analysis (using mris_glm) it seems to be the best to use a specific group average. Is there any "ready to use script" which I could use to build the average_study data and all the stuff needed by mris_glm?
3) Which files should be calculated to use them later for the stat. analysis and overlay?
Many thanks for your help!
Best wishes,
Philppe and Lukas
Lukas Scheef, MD, MSc MR-Tomography Department of Radiology University of Bonn Sigmund-Freud-Straße 25 D-53105 Bonn Fax: +49-228-287-5598 Phone:+49-228-287-4496 E-mail: L.Scheef@uni-bonn.de
in general you are better off making the average of your subjects, and displaying results on it, as it will more accurately reflect the true cross-subject registration. I've attached a script for doing so, make sure to set the SUBJECTS env variable to be the list of subjects you want to average, and it will create an "average" subject. Note that you don't need to rerun any morphing - this will use the current morph to build an average.
cheers, Bruce
On Fri, 27 Aug 2004 L.Scheef@uni-bonn.de wrote:
Dear list members!
I would like to analye cortical thickness data and wonder which is the best way to proceed...
So far I have processed the data using recon all (including manual top fixing). This includes the registration using the average7 subj. on the sphere.
- Is it a valid approach to use the coreg. on the average7 or should
I take a similar approach as used by VBM building a study specific template and do the coreg step on this template once again.
- For doing the cortical thickness group analysis (using mris_glm) it
seems to be the best to use a specific group average. Is there any "ready to use script" which I could use to build the average_study data and all the stuff needed by mris_glm?
- Which files should be calculated to use them later for the stat.
analysis and overlay?
Many thanks for your help!
Best wishes,
Philppe and Lukas
Lukas Scheef, MD, MSc MR-Tomography Department of Radiology University of Bonn Sigmund-Freud-Straße 25 D-53105 Bonn Fax: +49-228-287-5598 Phone:+49-228-287-4496 E-mail: L.Scheef@uni-bonn.de
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Thank you very much for sending the script. Unfortunately, the script does not run through... It stops at: ... cp $CSURF_DIR/average/$hemi.sphere.reg . ...
saying that there is no such file or directory:
cp: cannot stat '/usr/local/bin/freesurfer/average/lh.sphere.reg': No such file or directory
The directory exists, but the lh.sphere.reg does not...
Any idea what might get wrong?
Best wishes and many thanks in advance for your help!
Lukas
PS. I have defined the subject variable as set SUBJECTS=(FC_A FC_D FC_E ...) the rest of script is left untouched Datum: Fri, 27 Aug 2004 13:45:58 -0400 (EDT) Von: Bruce Fischl fischl@nmr.mgh.harvard.edu An: L.Scheef@uni-bonn.de Kopie an: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] cortical thickness stats.
in general you are better off making the average of your subjects, and displaying results on it, as it will more accurately reflect the true cross-subject registration. I've attached a script for doing so, make sure to set the SUBJECTS env variable to be the list of subjects you want to average, and it will create an "average" subject. Note that you don't need to rerun any morphing - this will use the current morph to build an average.
cheers, Bruce
On Fri, 27 Aug 2004 L.Scheef@uni-bonn.de wrote:
Dear list members!
I would like to analye cortical thickness data and wonder which is the best way to proceed...
So far I have processed the data using recon all (including manual top fixing). This includes the registration using the average7 subj. on the sphere.
- Is it a valid approach to use the coreg. on the average7 or should
I take a similar approach as used by VBM building a study specific template and do the coreg step on this template once again.
- For doing the cortical thickness group analysis (using mris_glm) it
seems to be the best to use a specific group average. Is there any "ready to use script" which I could use to build the average_study data and all the stuff needed by mris_glm?
- Which files should be calculated to use them later for the stat.
analysis and overlay?
Many thanks for your help!
Best wishes,
Philppe and Lukas
Lukas Scheef, MD, MSc MR-Tomography Department of Radiology University of Bonn Sigmund-Freud-Straße 25 D-53105 Bonn Fax: +49-228-287-5598 Phone:+49-228-287-4496 E-mail: L.Scheef@uni-bonn.de
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Lukas Scheef, MD, MSc MR-Tomography Department of Radiology University of Bonn Sigmund-Freud-Straße 25 D-53105 Bonn Fax: +49-228-287-5598 Phone:+49-228-287-4496 E-mail: L.Scheef@uni-bonn.de
sorry, that one bounced as it was too big. Try:
http://www.nmr.mgh.harvard.edu/~fischl
and click on the $FREESURFER_HOME/average/?h.sphere.reg link.
cheers, Bruce
On Mon, 30 Aug 2004 L.Scheef@uni-bonn.de wrote:
Hi Bruce,
Thank you very much for sending the script. Unfortunately, the script does not run through... It stops at: ... cp $CSURF_DIR/average/$hemi.sphere.reg . ...
saying that there is no such file or directory:
cp: cannot stat '/usr/local/bin/freesurfer/average/lh.sphere.reg': No such file or directory
The directory exists, but the lh.sphere.reg does not...
Any idea what might get wrong?
Best wishes and many thanks in advance for your help!
Lukas
PS. I have defined the subject variable as set SUBJECTS=(FC_A FC_D FC_E ...) the rest of script is left untouched Datum: Fri, 27 Aug 2004 13:45:58 -0400 (EDT) Von: Bruce Fischl fischl@nmr.mgh.harvard.edu An: L.Scheef@uni-bonn.de Kopie an: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] cortical thickness stats.
in general you are better off making the average of your subjects, and displaying results on it, as it will more accurately reflect the true cross-subject registration. I've attached a script for doing so, make sure to set the SUBJECTS env variable to be the list of subjects you want to average, and it will create an "average" subject. Note that you don't need to rerun any morphing - this will use the current morph to build an average.
cheers, Bruce
On Fri, 27 Aug 2004 L.Scheef@uni-bonn.de wrote:
Dear list members!
I would like to analye cortical thickness data and wonder which is the best way to proceed...
So far I have processed the data using recon all (including manual top fixing). This includes the registration using the average7 subj. on the sphere.
- Is it a valid approach to use the coreg. on the average7 or should
I take a similar approach as used by VBM building a study specific template and do the coreg step on this template once again.
- For doing the cortical thickness group analysis (using mris_glm) it
seems to be the best to use a specific group average. Is there any "ready to use script" which I could use to build the average_study data and all the stuff needed by mris_glm?
- Which files should be calculated to use them later for the stat.
analysis and overlay?
Many thanks for your help!
Best wishes,
Philppe and Lukas
Lukas Scheef, MD, MSc MR-Tomography Department of Radiology University of Bonn Sigmund-Freud-Straße 25 D-53105 Bonn Fax: +49-228-287-5598 Phone:+49-228-287-4496 E-mail: L.Scheef@uni-bonn.de
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Lukas Scheef, MD, MSc MR-Tomography Department of Radiology University of Bonn Sigmund-Freud-Straße 25 D-53105 Bonn Fax: +49-228-287-5598 Phone:+49-228-287-4496 E-mail: L.Scheef@uni-bonn.de
Many thanks!
Lukas
Datum: Mon, 30 Aug 2004 10:08:01 -0400 (EDT) Von: Bruce Fischl fischl@nmr.mgh.harvard.edu An: L.Scheef@uni-bonn.de Kopie an: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] cortical thickness stats.
sorry, that one bounced as it was too big. Try:
http://www.nmr.mgh.harvard.edu/~fischl
and click on the $FREESURFER_HOME/average/?h.sphere.reg link.
cheers, Bruce
On Mon, 30 Aug 2004 L.Scheef@uni-bonn.de wrote:
Hi Bruce,
Thank you very much for sending the script. Unfortunately, the script does not run through... It stops at: ... cp $CSURF_DIR/average/$hemi.sphere.reg . ...
saying that there is no such file or directory:
cp: cannot stat '/usr/local/bin/freesurfer/average/lh.sphere.reg': No such file or directory
The directory exists, but the lh.sphere.reg does not...
Any idea what might get wrong?
Best wishes and many thanks in advance for your help!
Lukas
PS. I have defined the subject variable as set SUBJECTS=(FC_A FC_D FC_E ...) the rest of script is left untouched Datum: Fri, 27 Aug 2004 13:45:58 -0400 (EDT) Von: Bruce Fischl fischl@nmr.mgh.harvard.edu An: L.Scheef@uni-bonn.de Kopie an: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] cortical thickness stats.
in general you are better off making the average of your subjects, and displaying results on it, as it will more accurately reflect the true cross-subject registration. I've attached a script for doing so, make sure to set the SUBJECTS env variable to be the list of subjects you want to average, and it will create an "average" subject. Note that you don't need to rerun any morphing - this will use the current morph to build an average.
cheers, Bruce
On Fri, 27 Aug 2004 L.Scheef@uni-bonn.de wrote:
Dear list members!
I would like to analye cortical thickness data and wonder which is the best way to proceed...
So far I have processed the data using recon all (including manual top fixing). This includes the registration using the average7 subj. on the sphere.
- Is it a valid approach to use the coreg. on the average7 or should
I take a similar approach as used by VBM building a study specific template and do the coreg step on this template once again.
- For doing the cortical thickness group analysis (using mris_glm) it
seems to be the best to use a specific group average. Is there any "ready to use script" which I could use to build the average_study data and all the stuff needed by mris_glm?
- Which files should be calculated to use them later for the stat.
analysis and overlay?
Many thanks for your help!
Best wishes,
Philppe and Lukas
Lukas Scheef, MD, MSc MR-Tomography Department of Radiology University of Bonn Sigmund-Freud-Straße 25 D-53105 Bonn Fax: +49-228-287-5598 Phone:+49-228-287-4496 E-mail: L.Scheef@uni-bonn.de
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Lukas Scheef, MD, MSc MR-Tomography Department of Radiology University of Bonn Sigmund-Freud-Straße 25 D-53105 Bonn Fax: +49-228-287-5598 Phone:+49-228-287-4496 E-mail: L.Scheef@uni-bonn.de
Lukas Scheef, MD, MSc MR-Tomography Department of Radiology University of Bonn Sigmund-Freud-Straße 25 D-53105 Bonn Fax: +49-228-287-5598 Phone:+49-228-287-4496 E-mail: L.Scheef@uni-bonn.de
p.s. all the thickness files should already have been generated when you did your surface recons.
On Fri, 27 Aug 2004 L.Scheef@uni-bonn.de wrote:
Dear list members!
I would like to analye cortical thickness data and wonder which is the best way to proceed...
So far I have processed the data using recon all (including manual top fixing). This includes the registration using the average7 subj. on the sphere.
- Is it a valid approach to use the coreg. on the average7 or should
I take a similar approach as used by VBM building a study specific template and do the coreg step on this template once again.
- For doing the cortical thickness group analysis (using mris_glm) it
seems to be the best to use a specific group average. Is there any "ready to use script" which I could use to build the average_study data and all the stuff needed by mris_glm?
- Which files should be calculated to use them later for the stat.
analysis and overlay?
Many thanks for your help!
Best wishes,
Philppe and Lukas
Lukas Scheef, MD, MSc MR-Tomography Department of Radiology University of Bonn Sigmund-Freud-Straße 25 D-53105 Bonn Fax: +49-228-287-5598 Phone:+49-228-287-4496 E-mail: L.Scheef@uni-bonn.de
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
L.Scheef＠uni-bonn.de