includes updated version of HCP pipeline!

installation:

Running

according to https://qunex.readthedocs.io/en/latest/wiki/Overview-QuickStart.html#option-b-step-by-step-execution

instead of dicom import use bids import:


qunex_container import_bids \\
    --sessionsfolder="${STUDY_FOLDER}/sessions" \\
    --inbox="${RAW_DATA}" \\
    --action='copy' \\
    --archive='leave' \\
    --overwrite=no \\
    --fileinfo=full \\
    --container="${QUNEX_CONTAINER}"

before qunex_container setup_hcp I neede to manualy modify /sessions/session_hcp.txt

1   :**T1w**                :run-01_T1w: DwellTime(9.8e-06)
2   :**T1w**                :run-02_T1w: DwellTime(9.8e-06)
3   :**T1w**                :run-03_T1w: DwellTime(9.8e-06)
4   :**T1w**                :run-04_T1w: DwellTime(9.8e-06)
5   :T2w             :T2w: UnwarpDir(x): DwellTime(2.7e-06): phenc(RL)

ERROR: Could not find folder with files for TOPUP processing of session KJ001_01.

        --hcp_avgrdcmethod (str):
            Averaging and readout distortion correction method.
            Can take the following values:

            **- 'NONE' (average any repeats with no readout correction)**
            - 'FIELDMAP' (average any repeats and use Siemens field map for
              readout correction)
            - 'SiemensFieldMap' (average any repeats and use Siemens field map
              for readout correction)
            - 'GEHealthCareFieldMap' (average any repeats and use GE field
              map for readout correction)
            - 'GEHealthCareLegacyFieldMap' (average any repeats and use GE field
              map for readout correction, for legacy, combined GE field maps)
            - 'PhilipsFieldMap' (average any repeats and use Philips field map
              for readout correction)
            - 'TOPUP' (average any repeats and use spin echo field map for
              readout correction).

What does it mean? If You want to perform fancy T1-T2 registration You need to provide fieldmaps… For a moment I select ‘None’ in the modified presurfer command as below:

qunex_container hcp_pre_freesurfer   --sessionsfolder="${STUDY_FOLDER}/sessio
ns"   --batchfile="${STUDY_FOLDER}/processing/batch.txt"   --container="${QUNEX_CONTAINER}" --hcp_avgrdcmet
hod=NONE **--hcp_avgrdcmethod=NONE**

Final touch - hcp transmit bias individual

Prepare WMGM mask

ml connectomeworkbench/1.5.0

wget <https://raw.githubusercontent.com/Washington-University/HCPpipelines/refs/heads/master/global/config/FreeSurferAllGMWM.txt>
wb_command -volume-label-import ./new-repo/sessions2/KJ001_01/hcp/KJ001_01/MNINonLinear/wmparc.nii.gz FreeSurferAllGMWM.txt ./new-repo/sessions2/KJ001_01/hcp/KJ001_01/MNINonLinear/WMGM.nii.gz -discard-others -drop-unused-labels