97bcda32d46ac2c2d8f97f9fe44ef8cdc3253710,pynets/registration/register.py,DmriReg,tissue2dwi_align,#DmriReg#,687

Before Change

                                                                   self.vent_csf_in_dwi))

        print("Creating Corpus Callosum mask...")
        os.system("fslmaths {} -mas {} -sub {} -bin {} 2>/dev/null".format(self.corpuscallosum_dwi,
                                                                           self.wm_in_dwi_bin,
                                                                           self.vent_csf_in_dwi,
                                                                           self.corpuscallosum_dwi))

        // Create gm-wm interface image
        os.system("fslmaths {} -mul {} -add {} -mas {} -bin {} 2>/dev/null".format(self.gm_in_dwi_bin,
                                                                                   self.wm_in_dwi_bin,
                                                                                   self.corpuscallosum_dwi,
                                                                                   self.B0_mask,
                                                                                   self.wm_gm_int_in_dwi))

        return

    def waymask2dwi_align(self, waymask):

After Change

        os.system(f"fslmaths {self.gm_in_dwi} -mas {self.gm_in_dwi_bin} {self.gm_in_dwi} 2>/dev/null")

        // Threshold CSF to binary in dwi space
        os.system(f"fslmaths {self.csf_mask_dwi} -mas {self.csf_mask_dwi_bin} {self.csf_mask_dwi} 2>/dev/null")

        // Create ventricular CSF mask
        print("Creating ventricular CSF mask...")
        os.system(f"fslmaths {self.vent_mask_dwi} -kernel sphere 10 -ero -bin {self.vent_mask_dwi} 2>/dev/null")
        os.system(f"fslmaths {self.csf_mask_dwi} -add {self.vent_mask_dwi} -bin {self.vent_csf_in_dwi} 2>/dev/null")

        print("Creating Corpus Callosum mask...")
        os.system(f"fslmaths {self.corpuscallosum_dwi} -mas {self.wm_in_dwi_bin} -sub {self.vent_csf_in_dwi} "
                  f"-bin {self.corpuscallosum_dwi} 2>/dev/null")

Instances