Doug,

Thanks for the quick reply.

At this point all I want to do is calculate average thickness, per group, then visualize the average whole brain thickness for each group. I’m thinking I’m probably going to need the latter option, but to clarify when I’m going to run mris_preproc the target is fsaverage and by --s will be averagesubject?

so

mris_preproc --s averagesubject --target fsaverage --hemi ?h --meas thickness --out new_averagesubject

?

jon On Apr 16, 2014, at 11:17 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

I'm not sure I understand what you mean. If you follow the group analysis wiki, it does not give you an option to even create an average subject, and you have to generate the average subject from make_average_subject. The proper path depends on what you want to do exactly.

If you want to do a full analysis on an average subject, then you'll need to create the average subject with make_average_subject. Then you will need to register your individuals to this subject with surfreg --s individual --t averagesubject ... Then run mris_preproc with --target averagesubject --surfreg averagesubject.sphere.reg

If you want to simply display the results on the average group anatomy, then run make_average_subject to create the average. Run mris_preproc using fsaverage. When you go to display the final result (eg, with tksurfer or freeview), specify the averagesubject instead of fsaverage

doug

On 04/16/2014 11:03 AM, Jonathan Holt wrote:

...

Hi all,

I’m currently trying to generate an average subject for two groups so that I might be able to display average thickness for both groups. I’m confused as to whether I should be following the GroupAnalysis workflow in the wiki, or if I should use make_average_subject and mris_preproc in tandem, but for the latter option (if it is the appropriate one) how should I use the two together, if that’s the right approach?

jon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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I'm a little lost here. Why would you run mris_preproc with the average subject as input? That is not one of the options I listed below. It sounds like you would run mris_preproc with fsaverage as the target and your list of subjects for a group as input. Then take the mean of the output stack to give you the group mean (mri_concat y.mgh --mean --o y.mean.mgh). Do this for each group. You can then display it on the average subject

doug

On 04/17/2014 11:22 AM, Jonathan Holt wrote:

Anyone have any input? On Apr 16, 2014, at 11:27 AM, Jonathan Holt whatsdac@umich.edu wrote:

...

Doug,

Thanks for the quick reply.

At this point all I want to do is calculate average thickness, per group, then visualize the average whole brain thickness for each group. I’m thinking I’m probably going to need the latter option, but to clarify when I’m going to run mris_preproc the target is fsaverage and by --s will be averagesubject?

so

mris_preproc --s averagesubject --target fsaverage --hemi ?h --meas thickness --out new_averagesubject

?

jon On Apr 16, 2014, at 11:17 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

...

I'm not sure I understand what you mean. If you follow the group analysis wiki, it does not give you an option to even create an average subject, and you have to generate the average subject from make_average_subject. The proper path depends on what you want to do exactly.

If you want to do a full analysis on an average subject, then you'll need to create the average subject with make_average_subject. Then you will need to register your individuals to this subject with surfreg --s individual --t averagesubject ... Then run mris_preproc with --target averagesubject --surfreg averagesubject.sphere.reg

If you want to simply display the results on the average group anatomy, then run make_average_subject to create the average. Run mris_preproc using fsaverage. When you go to display the final result (eg, with tksurfer or freeview), specify the averagesubject instead of fsaverage

doug

On 04/16/2014 11:03 AM, Jonathan Holt wrote:

...

Hi all,

I’m currently trying to generate an average subject for two groups so that I might be able to display average thickness for both groups. I’m confused as to whether I should be following the GroupAnalysis workflow in the wiki, or if I should use make_average_subject and mris_preproc in tandem, but for the latter option (if it is the appropriate one) how should I use the two together, if that’s the right approach?

jon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

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If you want to display the group mean on the average anatomy of your group, then you use make_average_subject. This is different that just creating an average map of cortical thickness (as is done with mris_preproc). make_average_subject actually creates surfaces, the whole freesurfer subject tree, etc. mris_preproc just creates a single file.

doug

On 04/17/2014 03:18 PM, Jon Holt wrote:

Doug

thank you for your patience. for you what seems natural can be a bit confusing for me. I'll do what you suggests, but I have to ask where does make_average_subject come into play. you recommended it as an option, but now it doesn't seem to be a part of the process

Jon

...

On Apr 17, 2014, at 3:08 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

I'm a little lost here. Why would you run mris_preproc with the average subject as input? That is not one of the options I listed below. It sounds like you would run mris_preproc with fsaverage as the target and your list of subjects for a group as input. Then take the mean of the output stack to give you the group mean (mri_concat y.mgh --mean --o y.mean.mgh). Do this for each group. You can then display it on the average subject

doug

...

On 04/17/2014 11:22 AM, Jonathan Holt wrote: Anyone have any input?

...

On Apr 16, 2014, at 11:27 AM, Jonathan Holt whatsdac@umich.edu wrote:

Doug,

Thanks for the quick reply.

At this point all I want to do is calculate average thickness, per group, then visualize the average whole brain thickness for each group. I’m thinking I’m probably going to need the latter option, but to clarify when I’m going to run mris_preproc the target is fsaverage and by --s will be averagesubject?

so

mris_preproc --s averagesubject --target fsaverage --hemi ?h --meas thickness --out new_averagesubject

?

jon

...

On Apr 16, 2014, at 11:17 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

I'm not sure I understand what you mean. If you follow the group analysis wiki, it does not give you an option to even create an average subject, and you have to generate the average subject from make_average_subject. The proper path depends on what you want to do exactly.

If you want to do a full analysis on an average subject, then you'll need to create the average subject with make_average_subject. Then you will need to register your individuals to this subject with surfreg --s individual --t averagesubject ... Then run mris_preproc with --target averagesubject --surfreg averagesubject.sphere.reg

If you want to simply display the results on the average group anatomy, then run make_average_subject to create the average. Run mris_preproc using fsaverage. When you go to display the final result (eg, with tksurfer or freeview), specify the averagesubject instead of fsaverage

doug

...

On 04/16/2014 11:03 AM, Jonathan Holt wrote: Hi all,

I’m currently trying to generate an average subject for two groups so that I might be able to display average thickness for both groups. I’m confused as to whether I should be following the GroupAnalysis workflow in the wiki, or if I should use make_average_subject and mris_preproc in tandem, but for the latter option (if it is the appropriate one) how should I use the two together, if that’s the right approach?

jon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/