Parcellation and Connectivity Usage

parc-con mode supports two parcellation backends — Chimera's multi-atlas fusion or a bundled MNI atlas — plus optional perturbation-based connectivity matrices computed from regional metabolite values.

Chimera parcellation

docker run --rm \
  -v /path/to/bids:/data:ro \
  -v /path/to/derivatives:/out \
  -v /path/to/freesurfer/license.txt:/opt/freesurfer/license.txt:ro \
  -e FS_LICENSE=/opt/freesurfer/license.txt \
  mrsiup/mrsiprep:cpu \
  /data /out participant \
  --participant-label S001 --session-label V1 \
  --metabolites CrPCr,GluGln,GPCPCh,NAANAAG,Ins \
  --ref-met CrPCr \
  --mode parc-con \
  --tissue-backend synthseg-fast \
  --parcellation-mode chimera \
  --chimera-scheme LFMIHIFIFF --chimera-scale 3

Chimera parcellation requires recon-all and a valid FS_LICENSE — mount a FreeSurfer license file as shown above. parc-con mode also writes a legacy-compatible parcel profile archive under <out>/mrsiprep/sub-*/ses-*/mrsi/parcel/*_desc-{GM,}metprofiles_mrsi.npz (GMmetprofiles when PVC ran, metprofiles when --no-pvc was passed).

Bundled MNI atlas

Use a bundled MNI atlas instead of Chimera (no FreeSurfer license required):

docker run --rm \
  -v /path/to/bids:/data:ro \
  -v /path/to/derivatives:/out \
  mrsiup/mrsiprep:cpu \
  /data /out participant \
  --participant-label S001 --session-label V1 \
  --metabolites CrPCr,GluGln,GPCPCh,NAANAAG,Ins \
  --ref-met CrPCr \
  --mode parc-con \
  --tissue-backend synthseg-fast \
  --parcellation-mode mni --atlas chimera-LFMIHIFIS-3

A custom atlas can be supplied with --custom-atlas and its lookup table with --custom-atlas-lut.

Regional metabolic profiles and connectivity

parc-con mode always builds a per-parcel regional metabolic profile for every retained parcel, regardless of --write-connectivity: each metabolite map is perturbed --connectivity-n-perturbations times with CRLB-scaled noise (--connectivity-sigma-scale) to propagate quantification uncertainty into the profile, then z-scored and averaged per parcel. This profile (written under <out>/mrsiprep/sub-*/ses-*/connectivity/*_desc-metabolicprofiles_mrsi.npz) is the standard regional derivative of parc-con mode and does not require --write-connectivity.

docker run --rm \
  -v /path/to/bids:/data:ro \
  -v /path/to/derivatives:/out \
  mrsiup/mrsiprep:cpu \
  /data /out participant \
  --participant-label S001 --session-label V1 \
  --metabolites CrPCr,GluGln,GPCPCh,NAANAAG,Ins \
  --ref-met CrPCr \
  --mode parc-con \
  --parcellation-mode mni --atlas chimera-LFMIHIFIS-3 \
  --write-connectivity \
  --connectivity-method spearman \
  --connectivity-space MNI

--write-connectivity is the optional add-on: it correlates the already-computed regional profiles into a regional connectivity (MetSiM) matrix, without recomputing the perturbations.

See Basic Usage for the full CLI reference, including --parcellation-mode, --atlas, --custom-atlas, --custom-atlas-lut, --chimera-scheme, --chimera-scale, --chimera-grow, --regional-summary, --write-connectivity, --connectivity-method, --connectivity-space, --connectivity-n-perturbations, --connectivity-sigma-scale, --connectivity-exclude-parcels, and --connectivity-max-parcel-id.