hcp_prep_long

qx_utilities.hcp.hcp_prep_long.hcp_prep_long(sinfo, options, overwrite=False, thread=0)

hcp_prep_long [... processing options]

Prepare the data for longitudinal processing with HCP longitudinal pipelines. Not needed if the starting point is hcp_long_freesurfer as that command does the prep work automatically.

For each subject in the batch file, QuNex will get their sessions and prepare a suitable subject folder by symlinking relevant folders into it. It will symlink both regular session folders and longitudinal sessions folders (defined by hcp_longitudinal_template) if they are present.

Parameters

--batchfile (str, default ''):

The batch.txt file with all the sessions information.

--sessionsfolder (str, default '.'):

The path to the study/sessions folder, where the imaging data is supposed to go.

--hcp_longitudinal_template (str, default 'base'):

Name of the longitudinal template.

--overwrite (str, default 'no'):

Whether to overwrite existing data (yes) or not (no). Note that previous data is deleted before the run, so in the case of a failed command run, previous results are lost.

--hcp_suffix (str, default ''):

Specifies a suffix to the session id if multiple variants are run, empty otherwise.

--logfolder (str, default ''):

The path to the folder where logs are to be stored, if other than default.

Output files

The results of this step will be present in the <study_folder>/subjects.

Examples

qunex hcp_prep_long \
    --sessionsfolder="<path_to_study_folder>/sessions" \
    --batchfile="<path_to_study_folder>/processing/batch.txt" \
    --hcp_longitudinal_template="base"