Table of Contents

7T Anatomical Acquisitions

Acquisition

The default anatomical acquisition for the 7T study is the calculated MP2RAGE UNI DEN (unified denoised, from 2 separate T1inv). But, in the middle of the study, the acquistion protocol was failing. So we collected a standard T1w mprage.

They have the same resolution but the mp2rage has better signal to noise. In some places the mprage is incorrectly annotated as acq-lowres. 

grep -hPo '/\S*nii.gz' /Volumes/Hera/preproc/7TBrainMech_rest/FS7.2/*res/1*_2*/scripts/recon-all.log |
  uniq | grep Raw |
  xargs 3dinfo -ad3 -iname|
  perl -pe 's:/.*?(highres|lowres)?_T1w.nii.gz:$1:i' |
  sort |uniq -c
    3 0.700005        0.687500        0.687500
  266 1.000000        1.000000        1.000000
   18 1.000000        1.000000        1.000000        lowres
    1 1.000000        1.000000        1.000008

Denoise Correction with SPM

see analysis_pipelinestructural_image_processing and SPM 

# build spm-latest.sif from docker://bids/spm:latest [Nov 15  2023]
/Volumes/Hera/Projects/corticalmyelin_development/code/corticalmyelin_maturation/software_installation/build_spm12_container.sh

# creates BIDS name-conforming background noise-removed and uniformity corrected T1w
/Volumes/Hera/Projects/corticalmyelin_development/BIDS/sub-*/ses-*/anat/*_acq-UNIDENT1corrected_T1w.nii.gz

# Used by ''/opt/ni_tools/preproc_pipelines/sources/7TBrainMechDenCrct_rest'' for preprocessing