It is trying to use the annotation when making the registration tif. This is hard coded in your version of make_average_surface. I've attached a new version. Run it with --no-annot. Let me know if it works and I'll check it into our distribution

doug

On 10/02/2014 12:00 AM, Reza Rajimehr wrote:

Hi Doug,

Step 1 did not generate "/iter00/lh.reg.template.tif" - though there was no obvious error for that on the screen. Not sure if this happened because of not having an annot file for mris_make_template. Here is what I saw on the screen:

%%%%%%%%%% /usr/local/freesurfer/bin/make_average_surface --subjects F99 --out iter00 --template-only --surf-reg sphere

$Id: make_average_surface,v 1.53.2.1 2011/05/25 20:53:44 greve Exp $ Wed Oct 1 23:00:55 EDT 2014 /home/reza/structurals setenv SUBJECTS_DIR /home/reza/structurals/ output ddir is /home/reza/structurals/ uid=1000(reza) gid=1000(reza) groups=1000(reza),4(adm),24(cdrom),27(sudo),30(dip),46(plugdev),108(lpadmin),124(sambashare) ==================== make_average_surface ==================== Wed Oct 1 23:00:56 EDT 2014 /home/reza/structurals /usr/local/freesurfer/bin/make_average_surface --subjects F99 --out iter00 --template-only --surf-reg sphere input subjects: F99 output subject: iter00 mri_add_xform_to_header -c auto /home/reza/structurals//iter00/mri/mni305.cor.mgz /home/reza/structurals//iter00/mri/mni305.cor.mgz INFO: extension is mgz

#@# Making lh registration template --------- /home/reza/structurals/iter00 mris_make_template -norot -annot aparc lh sphere F99 lh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject F99 (1 of 1) reading spherical surface /home/reza/structurals//F99/surf/lh.sphere... could not read annot file /home/reza/structurals//F99/surf/../label/lh.aparc.annot No such file or directory mris_make_template: could not read annot file aparc No such file or directory ERROR: cannot find /home/reza/structurals//iter00/lh.reg.template.tif ERROR: cannot find /home/reza/structurals//iter00/lh.reg.template.tif ERROR: cannot find /home/reza/structurals//iter00/lh.reg.template.tif %%%%%%%%%%

Reza

Hi Reza, I think that this should work. doug

set subjectlist = (subject1 subject2 ...)

1. Create a template from a single subject

make_average_surface --subjects $subjectlist[1] \ --out iter00 --template-only --surf-reg sphere.reg

2. Register each subject to this template, including first

subject. Each of these may take 30 min, so, if you have a lot of subjects, you may want to submit each job to the cluster.

foreach subject ($subjectlist) # Create subject/surf/iter00.sphere.reg, --no-annot for monkey surfreg --s $subject --t iter00 --no-annot end

3. Create a new template from all subjects using the new registration

make_average_surface --subjects $subjectlist \ --out iter01 --template-only --surf-reg iter00.sphere.reg

4. Register each subject to this new template

foreach subject ($subjectlist) # Create subject/surf/iter01.sphere.reg, --no-annot for monkey surfreg --s $subject --t iter01 --no-annot end

5. Return to step 3. Iterate 4 or 5 times to remove the dependence on

the first subject.

When using mri_surf2surf or mris_preproc, spec --surfreg iterXX.sphere.reg. For mris_preproc also spec --targ iterXX

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