No, unfortunately not. If all you want is the template, you can run mris_make_template to get the tif files. I think that's pretty fast. doug
On 5/9/11 10:42 PM, Joakim Vinberg wrote:
Doug, This is awesome--thank you! I have one final follow-up question, and maybe a bit of a long-shot: given that this process is a little time intensive, is make_average_subject able to "add in" extra subject to the existing template? E.g. If I've collected 10 subjects currently, but will shortly collect another 10--is the intermediate alignment information from the first 10 subjects saved anywhere that can be usefully used for the average subject of the final 20? Thanks again! Joakim
*From:* Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] *Sent:* Mon 5/9/2011 12:28 PM *To:* Joakim Vinberg; freesurfer *Subject:* Re: [Freesurfer] Making a custom experimental template
Hi Joakim,
here are some instructions on what to do (some of which you've already done):
doug
# Create an average subject (Creates $SUBJECTS_DIR/newtemplate) make_average_subject --out newtemplate --subjects subj1 subj2 subj3 ...
# Register each subject to the new template (do for both lh and rh) # Creates lh.sphere.reg.newtemplate and rh.sphere.reg.newtemplate foreach subject (subj1 subj2 subj3 ...) cd $SUBJECTS_DIR/subject mris_register -curv surf/lh.sphere \ $SUBJECTS_DIR/newtemplate/lh.reg.template.tif \ surf/lh.sphere.reg.newtemplate end
# Get thickness values in the newtemplate space for GLM analysis mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s subj3 ...
# Create another average template based on the previous one: # (Creates $SUBJECTS_DIR/newnewtemplate) make_average_subject --out newnewtemplate --surf-reg sphere.reg.newtemplate \ --subjects subj1 subj2 subj3 ...
Joakim Vinberg wrote:
Doug, Thanks! I just took a look at make_average_subject, and that looks quite a bit more streamlined--I think I'll just do that. Looking at make_average_subject, this should make the replacement for fsaverage. Following that, I would want to run mri_surf2surf to generate all of the surfaces in our new template space? Thanks! Joakim
*From:* Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] *Sent:* Fri 5/6/2011 9:46 AM *To:* Joakim Vinberg *Cc:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Making a custom experimental template
You are correct. If you run make_average_subject, it will create the template for you (as well as all the other files in a typical subject dir -- you'll need these to do a simple replacement for fsaverage).
doug
Joakim Vinberg wrote:
Hi FS crowd,
I just want to make sure that I have the process correctly described for setting up a custom experimental template. I am basing this off of the SurfaceRegAndTemplates (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates), and a hypothetical experiment with 10 subjects (s1, s2, ...s10). I
apologize
if this has been well-covered---I couldn't quite match it on the
website
or the archives.
For the prep step, I believe my commands would be:
mris_make_template lh sphere s1 custom_template_lh_0.tif
mris_make_template rh sphere s1 custom_template_rh_0.tif
which would result in two new template files names custom_template_lh_0.tif and custom_template_rh_0.tif
For Round 1, I would first create another registration for each
subject:
mris_register s1/surf/lh.sphere custom_template_lh_0.tif s1/surf/lh.sphere.regcustom_0
mris_register s1/surf/rh.sphere custom_template_rh_0.tif s1/surf/rh.sphere.regcustom_0
...
mris_register s10/surf/lh.sphere custom_template_lh_0.tif s10/surf/lh.sphere.regcustom_0
mris_register s10/surf/rh.sphere custom_template_rh_0.tif s10/surf/rh.sphere.regcustom_0
And then create another custom template:
mris_make_template lh sphere s1 s2 s3 ... s10 custom_template_lh_1.tif
mris_make_template rh sphere s1 s2 s3 ... s10 custom_template_rh_1.tif
For round 2, I would repeat Round 1, generating a new set of sphere.reg files, and then a new template, except substitute the custom template from round 1 (custom_template_lh_1.tif and custom_template_rh_1.tif).
Then, I would register all of my data to the custom_template_lh_2.tif and custom_template_rh_2.tif generated at the end of round 2. From there, I am assuming that I could be able to use this new template as I would fsaverage. Am I correct, or have I missed a step?
Thanks in advance for all of your help!
Joakim
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-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html