diff --git a/narps_open/pipelines/team_3C6G.py b/narps_open/pipelines/team_3C6G.py index ccebc659..b141188d 100644 --- a/narps_open/pipelines/team_3C6G.py +++ b/narps_open/pipelines/team_3C6G.py @@ -30,6 +30,7 @@ Level1Design, OneSampleTTestDesign, TwoSampleTTestDesign, EstimateModel, EstimateContrast, Threshold ) +from nipype.interfaces.spm.base import Info as SPMInfo from nipype.interfaces.fsl import ( ExtractROI ) @@ -265,12 +266,15 @@ def get_preprocessing(self): # 3 - Unified segmentation using tissue probability maps in SPM12. # Unified segmentation in SPM12 to MNI space (the MNI-space tissue probability maps used in segmentation) using default parameters. # Bias-field correction in the context of unified segmentation in SPM12. - tissue1 = [('/opt/spm12-r7771/spm12_mcr/spm12/tpm/TPM.nii', 1), 1, (True,False), (True, False)] - tissue2 = [('/opt/spm12-r7771/spm12_mcr/spm12/tpm/TPM.nii', 2), 1, (True,False), (True, False)] - tissue3 = [('/opt/spm12-r7771/spm12_mcr/spm12/tpm/TPM.nii', 3), 2, (True,False), (True, False)] - tissue4 = [('/opt/spm12-r7771/spm12_mcr/spm12/tpm/TPM.nii', 4), 3, (True,False), (True, False)] - tissue5 = [('/opt/spm12-r7771/spm12_mcr/spm12/tpm/TPM.nii', 5), 4, (True,False), (True, False)] - tissue6 = [('/opt/spm12-r7771/spm12_mcr/spm12/tpm/TPM.nii', 6), 2, (True,False), (True, False)] + # Get SPM Tissue Probability Maps file + spm_tissues_file = join(SPMInfo.getinfo()['path'], 'tpm', 'TPM.nii') + + tissue1 = [(spm_tissues_file, 1), 1, (True,False), (True, False)] + tissue2 = [(spm_tissues_file, 2), 1, (True,False), (True, False)] + tissue3 = [(spm_tissues_file, 3), 2, (True,False), (True, False)] + tissue4 = [(spm_tissues_file, 4), 3, (True,False), (True, False)] + tissue5 = [(spm_tissues_file, 5), 4, (True,False), (True, False)] + tissue6 = [(spm_tissues_file, 6), 2, (True,False), (True, False)] tissue_list = [tissue1, tissue2, tissue3, tissue4, tissue5, tissue6] segment = Node(