""" Get the values as mask from the neurosynth result """ lg = setLog._log(self.logf) lg.info('Doing mask_neurosynth_file') cmd = split("3dcalc -a %s -expr 'step(a)' \ -prefix %s " % (self.input, outfile)) lg.info("Command: \n%s" % cmd) p = subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) lg.info(p.stdout.decode("utf-8", "strict")) lg.info("Done with mask_neurosynth_file") if __name__ == '__main__': workdir = os.path.join('/Users/andric/Documents/workspace', 'AVPPI', 'nii', 'group_effects_dec') ns_masks = ['lateral_occipital_pFgA_z_FDR_0.01', 'mt_pFgA_z_FDR_0.01'] logs = os.path.join(workdir, 'mask_to_surface') for f in ns_masks: ms = mask_to_surface(os.path.join(workdir, '%s.nii.gz' % f), logs) outmask = os.path.join(workdir, 'stepmask_%s' % f) ms.mask_neurosynth_file(outmask) pn = 1.0 for hemi in ['lh', 'rh']: outname = '%s_%s_pn%s_MNI_N27.1D' % (outmask, hemi, pn) pr.vol2surf_mni(workdir, 'max_abs', hemi, '%s+tlrc' % outmask, pn, outname, logs, local=True)
@author: andric """ import os import procs as pr if __name__ == '__main__': effects = ['Aentr', 'Ventr', 'Aentr_intxn'] pn_list = ['1.0', '2.0'] mapping = 'max_abs' for block in [20, 15, 10]: outdir = os.path.join(os.environ['avp'], 'nii', 'group_effects_%sblk' % block) logf = os.path.join(outdir, 'project_to_surf') for ef in effects: if os.path.exists(os.path.join(os.environ['avp'], 'nii', 'group_effects_%sblk' % block, 'clust_%s_flt2_%sblk_msk_mema_mask+tlrc.BRIK.gz' % (ef, block))): parent_pref = os.path.join(outdir, 'clust_%s_flt2_%sblk_msk_mema' % (ef, block)) for hemi in ['lh', 'rh']: outname = '%s_%s_no_pn_MNI_N27.1D' % (parent_pref, hemi) pr.vol2surf_mni_no_pn(outdir, mapping, hemi, '%s+tlrc' % parent_pref, outname, logf) for pn in pn_list: outname = '%s_%s_pn%s_MNI_N27.1D' % (parent_pref, hemi, pn) pr.vol2surf_mni(outdir, mapping, hemi, '%s+tlrc' % parent_pref, pn, outname, logf)