27e4a648a96c76de6b7ed24ea95ea76ee17f623d,pynets/registration/register.py,FmriReg,atlas2t1wmni_align,#FmriReg#Any#Any#Any#,773

Before Change

        gm_mask_mni_img = nib.load(gm_mask_mni)
        if len(gm_mask_mni_img.header.extensions) != 0:
            gm_mask_mni_img.header.extensions.clear()
        nib.save(gm_mask_mni_img, gm_mask_mni)
        os.system("fslmaths {} -mas {} {}".format(aligned_atlas_t1mni, gm_mask_mni, aligned_atlas_t1mni_gm))

        atlas_img.uncache()
        img.uncache()

After Change

        from nilearn.image import resample_img
        aligned_atlas_t1mni = "%s%s%s%s" % (self.anat_path, "/", atlas, "_t1w_mni.nii.gz")
        gm_mask_mni = "%s%s%s%s" % (self.anat_path, "/", self.t1w_name, "_gm_mask_t1w_mni.nii.gz")
        gm_mask_mni_atlas_res = "%s%s%s%s%s" % (self.anat_path, "/", atlas, self.t1w_name, "_gm_mask_t1w_mni.nii.gz")
        aligned_atlas_t1mni_gm = "%s%s%s%s" % (self.anat_path, "/", atlas, "_t1w_mni_gm.nii.gz")

        uatlas_filled = "%s%s%s%s" % (self.anat_path, "/", atlas, "_filled.nii.gz")
        os.system("fslmaths {} -add {} -mas {} {}".format(self.input_mni_brain, uatlas, self.input_mni_mask,
                                                          uatlas_filled))

        regutils.align(uatlas_filled, self.t1_aligned_mni, init=None, xfm=self.atlas2t1wmni_xfm_init,
                       out=None, dof=12, searchrad=True, interp="nearestneighbour", cost="mutualinfo")

        if uatlas_parcels is not None:
            regutils.applyxfm(self.t1_aligned_mni, uatlas_parcels, self.atlas2t1wmni_xfm_init, aligned_atlas_t1mni,
                              interp="nearestneighbour")
        else:
            regutils.applyxfm(self.t1_aligned_mni, uatlas, self.atlas2t1wmni_xfm_init, aligned_atlas_t1mni,
                              interp="nearestneighbour")

        try:
            regutils.apply_warp(self.t1_aligned_mni, self.gm_mask_thr, gm_mask_mni, warp=self.warp_t1w2mni,
                                xfm=self.t12mni_xfm_init, interp="nn", sup=True)
        except:
            regutils.applyxfm(self.t1_aligned_mni, self.gm_mask_thr, self.t12mni_xfm_init, gm_mask_mni,
                              interp="nearestneighbour")

        // Set intensities to int
        atlas_img = nib.load(aligned_atlas_t1mni)
        gm_mask_img_res = resample_img(nib.load(gm_mask_mni), target_affine=atlas_img.affine,
                                       target_shape=atlas_img.shape)
        nib.save(gm_mask_img_res, gm_mask_mni_atlas_res)
        os.system("fslmaths {} -bin {}".format(gm_mask_mni_atlas_res, gm_mask_mni_atlas_res))
        os.system("fslmaths {} -mas {} {}".format(aligned_atlas_t1mni, gm_mask_mni_atlas_res, aligned_atlas_t1mni_gm))

        gm_mask_img_res.uncache()
        atlas_img.uncache()

Instances