Dear FreeSurfer experts,
I am trying to map volumetric ROIs obtained from VBM to surfaces in 5-6 year old children. I saw in a couple previous posts that it is recommended to run the template brain through recon-all, map the ROIs to the template surface, and then propagate the ROIs to all subjects using either mri_surf2surf, or (after turning the ROIs into labels) using mri_label2label.
The problem I have is that we used a custom age-appropriate template that will not pass through recon-all. I have tried using -notalairach & -notal-check.
Here is the output from the recon-all.log:
register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=24.0 skull bounding box = (128, 99, 138) --> (128, 154, 185) using (128, 117, 162) as brain centroid... mean wm in atlas = 126, using box (128,110,156) --> (127, 123,167) to find MRI wm WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255, mri_peak=-1 before smoothing, mri peak at 0 WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255, mri_peak=-1 after smoothing, mri peak at 0, scaling input intensities by inf Linux rc-twice 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s TOM_5yr_2 exited with ERRORS at Mon Feb 10 19:11:23 EST 2014
I am using version 5.3. Can you suggest any other options to get this template through recon-all?
Thanks in advance, Danielle