UNICORT

Unified segmentation based correction of R1 brain maps for RF transmit field inhomogeneities (UNICORT) (Weiskopf et al, 2011) is an algo available in SPM (also SPM BIDS App) to improve SNR of the MP2RAGE acquisition using an additional B1 acquisition a purely data driven approach.

We use this before running freesufer on

• 7T Anatomical Acquisitions

  /Volumes/Hera/Projects/corticalmyelin_development/code/corticalmyelin_maturation/image_processing/B1+_transmitfield_correction/unicort

  • Freesurfer for BrainMechR01 (7T) → fmriprep
  • Harnessing Quantitative MRI to Map Developmental Increases in Intracortical Myelin and their Biobehavioral Consequences
  • Environmental Impacts on Hippocampal Myelination
• SPA MR: /Volumes/Hera/Projects/SPA/pipeline_testing/scripts/mp2rage_processing

"/Volumes/Hera/Projects/SPA/scripts/mri/preproc/spm_unicort.m"

anat = spm_BIDS(bdir,'data', 'modality','anat', 'type','T1w'); % cell of file paths
if isempty(anat), error('Cannot find T1-weighted (UNIT1 as T1w) image in', bdir); end
 
% anat = cellfun(@(x)replace(x, '.gz',''), anat, 'Uni', 0)
 
matlabbatch{1}.spm.spatial.preproc.channel.vols  = cellstr(anat{1}); % cellstr not needed?
matlabbatch{1}.spm.spatial.preproc.channel.biasreg  = 0.001;
matlabbatch{1}.spm.spatial.preproc.channel.biasfwhm  = 60;
matlabbatch{1}.spm.spatial.preproc.channel.write  = [1, 1];
matlabbatch{1}.spm.spatial.preproc.warp.mrf = 1;
matlabbatch{1}.spm.spatial.preproc.warp.cleanup = 1;
matlabbatch{1}.spm.spatial.preproc.warp.reg = [0, 0.001, 0.5, 0.05, 0.2];
matlabbatch{1}.spm.spatial.preproc.warp.affreg = 'mni';
matlabbatch{1}.spm.spatial.preproc.warp.fwhm = 0;
matlabbatch{1}.spm.spatial.preproc.warp.samp = 3;
matlabbatch{1}.spm.spatial.preproc.warp.write = [0, 0];