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tools:unicort [2025/05/16 13:25] – created willtools:unicort [2026/02/03 11:09] (current) – add code and warning will
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 ====== UNICORT ====== ====== UNICORT ======
 **Unified segmentation based correction of R1 brain maps for RF transmit field inhomogeneities (UNICORT)** **Unified segmentation based correction of R1 brain maps for RF transmit field inhomogeneities (UNICORT)**
-([[https://pmc.ncbi.nlm.nih.gov/articles/PMC3018573/|Weiskopf  et al, 2011]]) is an algo available in [[:tools:spm]] to improve SNR of the [[:tools:mp2rage]] acquisition using an additional B1 acquisition. +([[https://pmc.ncbi.nlm.nih.gov/articles/PMC3018573/|Weiskopf  et al, 2011]]) is an algo available in [[:tools:spm]] (also [[:tools:spmbids]])  to improve SNR of the [[:tools:mp2rage]] acquisition using <del>an additional B1 acquisition</del> a purely data driven approach. 
  
 We use this before running [[:tools:freesufer]] on We use this before running [[:tools:freesufer]] on
   * [[:grants:7t:mr:anat]] <code>/Volumes/Hera/Projects/corticalmyelin_development/code/corticalmyelin_maturation/image_processing/B1+_transmitfield_correction/unicort</code>   * [[:grants:7t:mr:anat]] <code>/Volumes/Hera/Projects/corticalmyelin_development/code/corticalmyelin_maturation/image_processing/B1+_transmitfield_correction/unicort</code>
 +    * [[:grants:7t:mr:freesurfer]] -> [[:tools:fmriprep]]
 +    * [[:projects:mtrsnr]]
 +    * [[:projects:hpcmyelin]]
   * [[:grants:spa:mr]]: ''/Volumes/Hera/Projects/SPA/pipeline_testing/scripts/mp2rage_processing''   * [[:grants:spa:mr]]: ''/Volumes/Hera/Projects/SPA/pipeline_testing/scripts/mp2rage_processing''
 +  
 +
 +<WRAP important>Input images should be uncompressed nii files (not .nii.gz)</WRAP>
 +<code matlab "/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];
 +</code>