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t1-extensive - Skull-stripping of T1-weighted MR images in MNI standard space

This pipeline performs skull-stripping of T1-weighted MR images in Ixi549Space space using the brain mask (mask_ICV.nii) from the SPM software.

Prerequisites

You need to execute the t1-volume pipeline from Clinica to run this pipeline. Only the t1-volume-tissue-segmentation sub-pipeline ("Tissue segmentation, bias correction and spatial normalization to MNI space" step) needs to be executed.

Running the pipeline

The pipeline can be run with the following command line: 

clinicadl preprocessing run t1-extensive <caps_directory>
where:

  • caps_directory (str) is the input/output folder containing the results in a CAPS hierarchy.

Tip

type clinicadl preprocessing run t1-extensive --help to see the full list of parameters.

Outputs

Results are stored in the following folder of the CAPS hierarchy: subjects/sub-<participant_label>/ses-<session_label>/t1_extensive with the following outputs:

  • <source_file>_space-Ixi549Space_desc-SkullStripped_T1w.nii.gz: T1w image non-linearly registered to the Ixi549Space space and cropped.