recon-all -make all uses the unix 'make' utility, and the file $FREESURFER_HOME/bin/recon-all.makefile, to examine the 'build' dependencies between files. that is, looking at this table:

http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable

it can be seen that files are dependent on files that are 'older'. the recon-all.makefile defines those relationships that programmatically.

if it is running from the beginning for you, then some early file was modified, such that its timestamp became newer than a downstream file.

you can add -dontrun to the the end of recon-all -make all to see what it will run, w/o executing anything, to see what file is oldest.

n.

On Tue, 2010-02-16 at 12:08 -0500, Alessandro D. Gagliardi wrote:

Hello FreeSurfers,

recon-all -make is working now, but it's taking as long as it did the first time I ran it. I originally ran "recon-all -s cb -i CB_anat +org.BRIK -i CB_anat2+orig.BRIK -all" (for example) back in May and haven't messed with the results except for generating some label files with mri_annotation2label. I deleted the original BRIKs, but I don't see why that would matter in this case since the orig.mgz files are still there. Is it taking so long because so much has changed between 4.3 and 4.5, or is something wrong?

Thanks,

Alessandro D. Gagliardi Ph.D. Candidate Integrative Neuroscience Program Rutgers University Mind Brain Analysis adfgagliardi@gmail.com

P.S. To generate a2009s annotations files for fsaverage, do I just run "recon-all -s fsaverage -make all"?

On Sat, Feb 13, 2010 at 4:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Alessandro,

    usually that means that the smoothwm is out of date with the
    sphere.reg. You can run mris_euler_number on both to make sure
    they have the same number of vertices, faces and edges. Or you
    can just run

    recon-all -s $subject -make all

    which will rebuild things if it needs to

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