That is not unusual. It attempts to create an aseg by merging all the asegs from the individuals. To do this, it has to load all of them in memory, which often too big.
doug
Joakim Vinberg wrote:
Doug,
I figured that would be a little weird. Thanks again for guiding me through this process.
An additional follow-up question: this was the output from make_average_subject this morning. I have started mris_register, and it appears to be running just fine. Is this a normal error? If not, how best to get around it? I was running this on a MacPro with 8 cores and 16GB of memory—I’m surprised it would have ran out.
Thanks!
Joakim
nframestot = 307
Allocing output
mri_concat(32631) malloc: *** mmap(size=262144) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRIalloc(256, 256, 256): could not allocate 262144 bytes for 13726th slice
Cannot allocate memory
WARNING: could not create average segmentation for aseg ...
... but continuing
Tue May 10 06:31:38 PDT 2011
make_average_volume done
*From:* Douglas Greve [mailto:greve@nmr.mgh.harvard.edu] *Sent:* Monday, May 09, 2011 8:00 PM *To:* Joakim Vinberg; free surfer *Subject:* Re: [Freesurfer] Making a custom experimental template
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
mailto: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 mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto: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 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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